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Conserved domains on  [gi|767965830|ref|XP_011518376|]
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natural cytotoxicity triggering receptor 3 ligand 1 isoform X2 [Homo sapiens]

Protein Classification

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List of domain hits

Name Accession Description Interval E-value
IgV_B7-H6 cd20981
Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the ...
1-110 3.12e-78

Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the immunoglobulin variable (IgV) domain of B7-H6 (also known as NCR3LG1). B7-H6 contains one IgV domain and one IgC domain (IgV-IgC) and belongs to the B7-family, which consists of structurally related cell-surface protein ligands which bind to receptors on lymphocytes that regulate immune responses. B7-H6 is a ligand of NKp30, which is a member of CD28 family and an activating receptor of natural killer (NK) cells. The expression of NKp30 has been found in most of NK cells, which is involved in the process of tumor cell killing and interaction with antigen presenting cells (APCs) such as dendritic cells. Studies showed that NK cells eliminate B7-H6-expressing tumor cells either directly via cytotoxicity or indirectly by cytokine secretion. For instance, chimeric NKp30-expressing T cells responded to B7-H6(+) tumor cells and those T cells produced IFN-gamma and killed B7-H6-expressing tumor cells in vivo. B7-H6 mRNA is not found in normal cells, while high expression of B7-H6 is found in certain type tumor cells, such as lymphoma, leukemia, ovarian cancer, brain tumors, breast cancers, and various sarcomas. Since B7-H6 can bind NKp30 to exert anti-tumor effects by NK cells, which are able to recognize the difference between cancer cells and normal cells, B7-H6 may serve as a promising target for cancer immunotherapy.


:

Pssm-ID: 409573  Cd Length: 114  Bit Score: 237.51  E-value: 3.12e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830   1 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFWKSLTFDKEVKVFEFFGDHQEAFRPGAIVSPWRLKSGDASLRL 80
Cdd:cd20981    5 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFRKSLTFDKEVKVFEFFGDHQKAFRPGAIVSPWRLKSGDASLQL 84
                         90       100       110
                 ....*....|....*....|....*....|
gi 767965830  81 PGIQLEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:cd20981   85 PGVQLEEAGEYRCEVVVTPLKAQGTVQLEV 114
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
109-214 4.13e-23

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


:

Pssm-ID: 409354  Cd Length: 95  Bit Score: 92.91  E-value: 4.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 109 EVVASPASRLLldqvgMKENEDKYMCESSGFYPEAINITWEKQTQKFPHpieiseDVITGPTIKNMDGTFNVTSCLKLNS 188
Cdd:cd00098    1 TVTLLPPSPEE-----KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTS------GVSTSSPVEPNDGTYSVTSSLTVPP 69
                         90       100
                 ....*....|....*....|....*.
gi 767965830 189 SQEDPGTVYQCVVRHASLHTPLRSNF 214
Cdd:cd00098   70 SDWDEGATYTCVVTHESLKSPLSKTW 95
 
Name Accession Description Interval E-value
IgV_B7-H6 cd20981
Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the ...
1-110 3.12e-78

Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the immunoglobulin variable (IgV) domain of B7-H6 (also known as NCR3LG1). B7-H6 contains one IgV domain and one IgC domain (IgV-IgC) and belongs to the B7-family, which consists of structurally related cell-surface protein ligands which bind to receptors on lymphocytes that regulate immune responses. B7-H6 is a ligand of NKp30, which is a member of CD28 family and an activating receptor of natural killer (NK) cells. The expression of NKp30 has been found in most of NK cells, which is involved in the process of tumor cell killing and interaction with antigen presenting cells (APCs) such as dendritic cells. Studies showed that NK cells eliminate B7-H6-expressing tumor cells either directly via cytotoxicity or indirectly by cytokine secretion. For instance, chimeric NKp30-expressing T cells responded to B7-H6(+) tumor cells and those T cells produced IFN-gamma and killed B7-H6-expressing tumor cells in vivo. B7-H6 mRNA is not found in normal cells, while high expression of B7-H6 is found in certain type tumor cells, such as lymphoma, leukemia, ovarian cancer, brain tumors, breast cancers, and various sarcomas. Since B7-H6 can bind NKp30 to exert anti-tumor effects by NK cells, which are able to recognize the difference between cancer cells and normal cells, B7-H6 may serve as a promising target for cancer immunotherapy.


Pssm-ID: 409573  Cd Length: 114  Bit Score: 237.51  E-value: 3.12e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830   1 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFWKSLTFDKEVKVFEFFGDHQEAFRPGAIVSPWRLKSGDASLRL 80
Cdd:cd20981    5 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFRKSLTFDKEVKVFEFFGDHQKAFRPGAIVSPWRLKSGDASLQL 84
                         90       100       110
                 ....*....|....*....|....*....|
gi 767965830  81 PGIQLEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:cd20981   85 PGVQLEEAGEYRCEVVVTPLKAQGTVQLEV 114
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
109-214 4.13e-23

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 92.91  E-value: 4.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 109 EVVASPASRLLldqvgMKENEDKYMCESSGFYPEAINITWEKQTQKFPHpieiseDVITGPTIKNMDGTFNVTSCLKLNS 188
Cdd:cd00098    1 TVTLLPPSPEE-----KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTS------GVSTSSPVEPNDGTYSVTSSLTVPP 69
                         90       100
                 ....*....|....*....|....*.
gi 767965830 189 SQEDPGTVYQCVVRHASLHTPLRSNF 214
Cdd:cd00098   70 SDWDEGATYTCVVTHESLKSPLSKTW 95
IGc1 smart00407
Immunoglobulin C-Type;
134-209 1.82e-12

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 62.33  E-value: 1.82e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767965830   134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTP 209
Cdd:smart00407   6 CLVSGFYPPDITVTWLRNGQ------EVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
133-206 3.10e-12

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 61.88  E-value: 3.10e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767965830  133 MCESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASL 206
Cdd:pfam07654  18 TCLVTGFYPPDITVTWLKNGQ------EVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHEGL 85
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
5-110 1.91e-05

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 42.88  E-value: 1.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830     5 GTQITPLNDNVTIFCNIFYSQPLNITsmgitWFWKSLTFDKEVKVFEFFGDhqeafrpgaivspwrlkSGDASLRLPGIQ 84
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGSPPPEVT-----WYKQGGKLLAESGRFSVSRS-----------------GSTSTLTISNVT 59
                           90       100
                   ....*....|....*....|....*.
gi 767965830    85 LEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:smart00410  60 PEDSGTYTCAATNSSGSASSGTTLTV 85
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
9-111 2.02e-04

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 40.52  E-value: 2.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830    9 TPLNDNVTIFCniFYSQPLNITSMGITWFWKSLTFDKEVKVFEFfGDHQEAFRPGAIVSpWR--LKSGDASLRLPGIQLE 86
Cdd:pfam07686   8 VALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIAYY-SNGSEEGVKKGRFS-GRgdPSNGDGSLTIQNLTLS 83
                          90       100
                  ....*....|....*....|....*.
gi 767965830   87 EAGEYRCEVVVTP-LKAQGTVQLEVV 111
Cdd:pfam07686  84 DSGTYTCAVIPSGeGVFGKGTRLTVL 109
 
Name Accession Description Interval E-value
IgV_B7-H6 cd20981
Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the ...
1-110 3.12e-78

Immunoglobulin variable (IgV) domain of B7-H6; The members here are composed of the immunoglobulin variable (IgV) domain of B7-H6 (also known as NCR3LG1). B7-H6 contains one IgV domain and one IgC domain (IgV-IgC) and belongs to the B7-family, which consists of structurally related cell-surface protein ligands which bind to receptors on lymphocytes that regulate immune responses. B7-H6 is a ligand of NKp30, which is a member of CD28 family and an activating receptor of natural killer (NK) cells. The expression of NKp30 has been found in most of NK cells, which is involved in the process of tumor cell killing and interaction with antigen presenting cells (APCs) such as dendritic cells. Studies showed that NK cells eliminate B7-H6-expressing tumor cells either directly via cytotoxicity or indirectly by cytokine secretion. For instance, chimeric NKp30-expressing T cells responded to B7-H6(+) tumor cells and those T cells produced IFN-gamma and killed B7-H6-expressing tumor cells in vivo. B7-H6 mRNA is not found in normal cells, while high expression of B7-H6 is found in certain type tumor cells, such as lymphoma, leukemia, ovarian cancer, brain tumors, breast cancers, and various sarcomas. Since B7-H6 can bind NKp30 to exert anti-tumor effects by NK cells, which are able to recognize the difference between cancer cells and normal cells, B7-H6 may serve as a promising target for cancer immunotherapy.


Pssm-ID: 409573  Cd Length: 114  Bit Score: 237.51  E-value: 3.12e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830   1 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFWKSLTFDKEVKVFEFFGDHQEAFRPGAIVSPWRLKSGDASLRL 80
Cdd:cd20981    5 MMAGGTQITPLNDNVTIFCNIFYSQPLNITSMGITWFRKSLTFDKEVKVFEFFGDHQKAFRPGAIVSPWRLKSGDASLQL 84
                         90       100       110
                 ....*....|....*....|....*....|
gi 767965830  81 PGIQLEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:cd20981   85 PGVQLEEAGEYRCEVVVTPLKAQGTVQLEV 114
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
109-214 4.13e-23

Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, classical Ig-like domains resembling the antibody constant domain. Members of the IgC1 family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, while the IgC domain is involved in oligomerization and molecular interactions. The structures in C1-set are smaller than those in the V-set; they have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409354  Cd Length: 95  Bit Score: 92.91  E-value: 4.13e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 109 EVVASPASRLLldqvgMKENEDKYMCESSGFYPEAINITWEKQTQKFPHpieiseDVITGPTIKNMDGTFNVTSCLKLNS 188
Cdd:cd00098    1 TVTLLPPSPEE-----KGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTS------GVSTSSPVEPNDGTYSVTSSLTVPP 69
                         90       100
                 ....*....|....*....|....*.
gi 767965830 189 SQEDPGTVYQCVVRHASLHTPLRSNF 214
Cdd:cd00098   70 SDWDEGATYTCVVTHESLKSPLSKTW 95
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
114-211 5.62e-15

Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain on Tapasin-R. Tapasin is a V-C1 (variable-constant) immunoglobulin superfamily molecule present in the endoplasmic reticulum (ER), where it links MHC class I molecules to the transporter associated with antigen processing (TAP). Tapasin-R is a tapasin-related protein that contains similar structural motifs to Tapasin, with some marked differences, especially in the V domain, transmembrane and cytoplasmic regions. The majority of Tapasin-R is located within the ER; however, there may be some expression of Tapasin-R at the cell surface. Tapasin-R lacks an obvious ER retention signal.


Pssm-ID: 409428  Cd Length: 100  Bit Score: 70.22  E-value: 5.62e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 114 PASRLLLDQVGMKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDP 193
Cdd:cd05771    1 PRVRLSPKNLVKPDLPQTLSCHIAGYYPLDVDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEPGTENR 80
                         90
                 ....*....|....*...
gi 767965830 194 GTVYQCVVRHASLHTPLR 211
Cdd:cd05771   81 GATYTCRVTHVSLEEPLS 98
IGc1 smart00407
Immunoglobulin C-Type;
134-209 1.82e-12

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 62.33  E-value: 1.82e-12
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767965830   134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTP 209
Cdd:smart00407   6 CLVSGFYPPDITVTWLRNGQ------EVTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75
C1-set pfam07654
Immunoglobulin C1-set domain;
133-206 3.10e-12

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 61.88  E-value: 3.10e-12
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 767965830  133 MCESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASL 206
Cdd:pfam07654  18 TCLVTGFYPPDITVTWLKNGQ------EVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCRVEHEGL 85
IgC1_CH3_IgAGD_CH4_IgAEM cd05768
CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, ...
134-212 1.71e-10

CH3 domain (third constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, gamma, and delta chains, and CH4 domain (fourth constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, epsilon, and mu chains; member of the C1-set of I; The members here are composed of the third and fourth immunoglobulin constant domain (IgC) of alpha, delta, gamma and alpha, epsilon, and mu heavy chains, respectively. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409425  Cd Length: 105  Bit Score: 57.73  E-value: 1.71e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767965830 134 CESSGFYPEAINITWEKQTQKFPhpieiSEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTPLRS 212
Cdd:cd05768   23 CLVKGFYPEDIFVSWLQNGEPLP-----SADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDVFSCVVGHEALPLQFTQ 96
Ig_LP_like cd05877
Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The ...
13-107 4.46e-10

Immunoglobulin (Ig)-like domain of human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in human cartilage link protein (LP; also called hyaluronan and proteoglycan link protein). In cartilage, chondroitin-keratan sulfate proteoglycan (CSPG), aggrecan, forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409461  Cd Length: 117  Bit Score: 56.95  E-value: 4.46e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  13 DNVTIFCNIFYSQPLNITS-MGITWFWKSLTFDKEVKVFEFFGDHQEAF-RPGAIVSPWRLKSGDASLRLPGIQLEEAGE 90
Cdd:cd05877   13 GNVTLPCRYHYEPELSAPRkIRVKWTKLEVDYAKEEDVLVAIGTRHKSYgSYQGRVFLRRADDLDASLVITDLRLEDYGR 92
                         90       100
                 ....*....|....*....|....*
gi 767965830  91 YRCEV--------VVTPLKAQGTVQ 107
Cdd:cd05877   93 YRCEVidgledesVVVALRLRGVVF 117
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
134-215 3.77e-08

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II beta chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain has two globular domains (N- and C-terminal) and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409423  Cd Length: 96  Bit Score: 50.79  E-value: 3.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSqedPGTVYQCVVRHASLHTPLRSN 213
Cdd:cd05766   24 CSVTGFYPAEIEVKWFRNGQ------EETAGVVSTELIPNGDWTFQILVMLETTPR---RGDVYTCQVEHSSLQSPLTVD 94

                 ..
gi 767965830 214 FT 215
Cdd:cd05766   95 WR 96
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
134-210 8.92e-08

Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Cluster of Differentiation (CD) 1. CD1 family of transmembrane glycoproteins, are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. They mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes (CD1a, CD1b, CD1c, CD1d, and CD1e) organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. CD1a localizes to the plasma membrane and to recycling vesicles of the early endocytic system. Alternative splicing results in multiple transcript variants. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. C1-set Ig domains have one beta sheet that is formed by strands A, B, E, and D and the other strands by G, F, C, and C'.


Pssm-ID: 409620  Cd Length: 93  Bit Score: 49.63  E-value: 8.92e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNssqEDPGTVYQCVVRHASLHTPL 210
Cdd:cd21029   22 CHVTGFYPRPIEVTWLRDGQ------EQMDGTQSGGILPNHDGTYQLRKTLDIA---PGEGAGYSCRVDHSSLKQDL 89
IgC1_MHC_I_alpha3 cd07698
Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; ...
134-214 1.24e-07

Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I alpha chain. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409495  Cd Length: 92  Bit Score: 49.15  E-value: 1.24e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPgtvYQCVVRHASLHTPLRSN 213
Cdd:cd07698   21 CWALGFYPAEITLTWQRDGE------DQTQDMELVETRPNGDGTFQKWAAVVVPSGEEQR---YTCHVQHEGLPEPLTLR 91

                 .
gi 767965830 214 F 214
Cdd:cd07698   92 W 92
IgC1_L cd07699
Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) ...
134-214 1.41e-07

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.


Pssm-ID: 409496  Cd Length: 99  Bit Score: 49.38  E-value: 1.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTPLRSN 213
Cdd:cd07699   23 CLINKFYPGFATVTWKVDGS------TVSSGVTTSKTEQQSDNTYSMSSYLTLSSSDWNKHKVYTCEVTHEGLSSTITKS 96

                 .
gi 767965830 214 F 214
Cdd:cd07699   97 F 97
IgC1_CH1_IgADEGM cd04985
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, ...
134-205 6.16e-07

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha, delta, epsilon, gamma, and mu chains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha, delta, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409374  Cd Length: 98  Bit Score: 47.58  E-value: 6.16e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767965830 134 CESSGFYPEAINITWEKQTQKfphpiEISEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHAS 205
Cdd:cd04985   23 CLISDYFPESITVSWQKNTNS-----ITSGFTRTFPVVLRSGGDYSCSSQLTVPLQEWNSGEVYKCQVQHSA 89
IgC1_MHC_II_beta_HLA-DP cd21003
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
106-210 1.22e-06

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DP. HLA class II histocompatibility antigen, DP(W2) beta chain is a protein that in humans is encoded by the HLA-DPB1 gene. It plays a central role in the immune system by presenting peptides derived from extracellular proteins. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DP is an alphabeta heterodimer cell-surface receptor. Each DP subunit (alpha-subunit, beta-subunit) is composed of a alpha-helical N-terminal domain, an IgG-like beta sheet, a membrane spanning domain, and a cytoplasmic domain. The alpha-helical domain forms the sides of the peptide binding groove. The beta sheet regions form the base of the binding groove and the bulk of the molecule as well as the inter-subunit (non-covalent) binding region. Individuals carrying the MHCII allele, HLA-DP2, are at risk for chronic beryllium disease (CBD), a debilitating inflammatory lung condition caused by the reaction of CD4 T cells to inhaled beryllium. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409594  Cd Length: 96  Bit Score: 46.67  E-value: 1.22e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 106 VQLEVVASPASRLLLdqvgmkENEDKYMCESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLK 185
Cdd:cd21003    2 VQPKVNVSPSKKGPL------QHHNLLVCHVTDFYPGNIQVRWFLNGQ------EETAGVVSTNLIHNGDWTFQILVMLE 69
                         90       100
                 ....*....|....*....|....*
gi 767965830 186 LNSSQedpGTVYQCVVRHASLHTPL 210
Cdd:cd21003   70 MTPQQ---GDVYTCQVEHPSLDSPV 91
IgI_2_Necl-1 cd07705
Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set ...
125-212 1.45e-06

Second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molcule-1 (Necl-1; also known as cell adhesion molecule3 (CADM3)). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains is essential to cell-cell adhesion and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 409502  Cd Length: 103  Bit Score: 46.50  E-value: 1.45e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 125 MKENEDKYM-CESSGFYPEAiNITWEKQTQKFP-HPIEISEDVitgptiknMDGTFNVTSCLKLNSSQEDPGTVYQCVVR 202
Cdd:cd07705   16 FKEKDKAKLrCTSSGSKPAA-NIKWRKGDQELEgAPTSVQEDG--------NGKTFTVSSSVEFQVTREDDGAEITCSVG 86
                         90
                 ....*....|
gi 767965830 203 HASLHTPLRS 212
Cdd:cd07705   87 HESLHDSDRS 96
IgC1_SIRP_domain_3 cd16085
Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig ...
122-203 1.91e-06

Signal-regulatory protein (SIRP) immunoglobulin-like domain 3; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 3 (C1 repeat 2). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains a single V-set and two C1-set IgSF domains. Their cytoplasmic tails that contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs but also binds CD47, but with much less affinity.


Pssm-ID: 409507  Cd Length: 96  Bit Score: 45.88  E-value: 1.91e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 122 QVGMKENEDKYMCESSGFYPEAINITW-----EKQTQKFPHPIEisedvitgptikNMDGTFNVTSCLKLNSSQEDPGTV 196
Cdd:cd16085   10 QPTMVWNQVNVTCQVEKFYPQRLQLTWlengnVSRTETPSTLTV------------NKDGTYNWTSWLLVNVSAHREDVV 77

                 ....*..
gi 767965830 197 YQCVVRH 203
Cdd:cd16085   78 LTCQVEH 84
IgC1_MHC_II_beta_HLA-DR cd21000
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
133-210 6.08e-06

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DR. HLA-DR is an MHC class II cell surface receptor encoded by the human leukocyte antigen complex on chromosome 6 region 6p21.31. HLA-DR is also involved in several autoimmune conditions, disease susceptibility, and disease resistance including seronegative-rheumatoid arthritis, penicillamine-induced myasthenia, schizophrenia, Goodpasture syndrome, systemic lupus erythematosus, Alzheimers, tuberculoid leprosy, and Hashimoto's thyroiditis. HLA-DR molecules are upregulated in response to signaling. HLA-DR is an alphabeta heterodimer cell surface receptor, each subunit of which contains two extracellular domains, a membrane-spanning domain, and a cytoplasmic tail. Both alpha and beta chains are anchored in the membrane. The DR beta chain is encoded by 4 loci, however no more than 3 functional loci are present in a single individual, and no more than two on a single chromosome. Sometimes an individual may only possess 2 copies of the same locus, DRB1*. The HLA-DRB1 locus is ubiquitous and encodes a very large number of functionally variable gene products (HLA-DR1 to HLA-DR17). The HLA-DRB3 locus encodes the HLA-DR52 specificity, is moderately variable and is variably associated with certain HLA-DRB1 types. The HLA-DRB4 locus encodes the HLA-DR53 specificity, has some variation, and is associated with certain HLA-DRB1 types. The HLA-DRB5 locus encodes the HLA-DR51 specificity, which is typically invariable, and is linked to the HLA-DR2 types. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409591  Cd Length: 96  Bit Score: 44.61  E-value: 6.08e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767965830 133 MCESSGFYPEAINITWEKQTQkfphpiEISEDVITGPTIKNMDGTFNVTSCLKlnsSQEDPGTVYQCVVRHASLHTPL 210
Cdd:cd21000   23 VCSVNGFYPGSIEVRWFRNGQ------EEKAGVVSTGLIQNGDWTFQTLVMLE---TVPRSGEVYTCQVEHPSVTSPL 91
IgC1_MHC_II_beta_HLA-DM cd21002
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
134-215 1.23e-05

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DM. Human HLA-DM plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. Type 1 diabetes is correlated with DM activation and it is also implicated in viral infections such as herpes simplex virus, celiac disease, multiple sclerosis, other autoimmune diseases, and leukemia. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409593  Cd Length: 97  Bit Score: 43.76  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphPIEISEdviTGPT--IKNMDGTFNVTSCLKLNSSqedPGTVYQCVVRHASLHTPLR 211
Cdd:cd21002   24 CHVWGFYPADVTITWLKNGD----PVAPHS---SAPKtaQPNGDWTYQTQVTLAVTPS---PGDTYTCSVQHASLPEPLL 93

                 ....
gi 767965830 212 SNFT 215
Cdd:cd21002   94 EDWT 97
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
5-110 1.91e-05

Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 42.88  E-value: 1.91e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830     5 GTQITPLNDNVTIFCNIFYSQPLNITsmgitWFWKSLTFDKEVKVFEFFGDhqeafrpgaivspwrlkSGDASLRLPGIQ 84
Cdd:smart00410   2 PSVTVKEGESVTLSCEASGSPPPEVT-----WYKQGGKLLAESGRFSVSRS-----------------GSTSTLTISNVT 59
                           90       100
                   ....*....|....*....|....*.
gi 767965830    85 LEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:smart00410  60 PEDSGTYTCAATNSSGSASSGTTLTV 85
IgC1_SIRP_domain_2 cd05772
Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig ...
110-216 2.06e-05

Signal-regulatory protein (SIRP) immunoglobulin-like domain 2; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig)-like domain in Signal-Regulatory Protein (SIRP), domain 2 (C1 repeat 1). The SIRPs belong to the "paired receptors" class of membrane proteins that comprise several genes coding for proteins with similar extracellular regions, but very different transmembrane/cytoplasmic regions with different (activating or inhibitory) signaling potentials. They are commonly on NK cells, but are also on many myeloid cells. Their extracellular region contains three Immunoglobulin superfamily domains, a single V-set and two C1-set IgSF domains. Their cytoplasmic tails contain either ITIMs or transmembrane regions that have positively charged residues that allow an association with adaptor proteins, such as DAP12/KARAP, containing ITAMs. There are 3 distinct SIRP members: alpha, beta, and gamma. SIRP alpha (also known as CD172a or SRC homology 2 domain-containing protein tyrosine phosphatase substrate 1/Shps-1) is a membrane receptor that interacts with a ligand CD47 expressed on many cells and gives an inhibitory signal through immunoreceptor tyrosine-based inhibition motifs in the cytoplasmic region that interact with phosphatases SHP-1 and SHP-2. SIRP beta has a short cytoplasmic region and associates with a transmembrane adapter protein DAP12 containing immunoreceptor tyrosine-based activation motifs to give an activating signal. SIRP gamma contains a very short cytoplasmic region lacking obvious signaling motifs, but also binds CD47, but with much less affinity.


Pssm-ID: 409429  Cd Length: 102  Bit Score: 43.08  E-value: 2.06e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 110 VVASPASRLlldQVGMKENedkYMCESSGFYPEAINITWEK--------QTQKFPHPIEISedvitgptiknmdgtFNVT 181
Cdd:cd05772    6 LVSGPSGRA---TPGQTVS---FTCKSHGFSPRDITLKWFKngnelsalQTTVFPEGDSVS---------------YSVS 64
                         90       100       110
                 ....*....|....*....|....*....|....*
gi 767965830 182 SCLKLNSSQEDPGTVYQCVVRHASLHTPLRSNFTL 216
Cdd:cd05772   65 STVQVVLTKDDVHSQLTCEVAHVTLQAPLRGTANL 99
IgC1_CH2_Mu cd16093
CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member ...
133-208 4.33e-05

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin mu chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin constant domain (IgC) of mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409513  Cd Length: 99  Bit Score: 42.00  E-value: 4.33e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767965830 133 MCESSGFYPEAINITWEKQTQKFPHpieiSEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHT 208
Cdd:cd16093   23 VCLATGFSPKTISFKWLRNGKEVTS----STGAVVEEPKEDGKTLYSATSFLTITESEWKSQTEFTCEFKHKGEIV 94
IgI_2_Necl-1-4 cd05761
Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of ...
134-206 8.41e-05

Second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 - Necl-4; member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 or CADM3), Necl-2 (also known as CADM1), Necl-3 (also known as CADM2) and Necl-4 (also known as CADM4). These nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1 and Necl-2 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues, and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system, where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Necl-4 is expressed on Schwann cells, and plays a key part in initiating peripheral nervous system (PNS) myelination. Necl-4 participates in cell-cell adhesion and is proposed to play a role in tumor suppression.


Pssm-ID: 409418  Cd Length: 102  Bit Score: 41.26  E-value: 8.41e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767965830 134 CESSGFYPEAiNITWEKQTQKFPHPIEISEDvitgptikNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASL 206
Cdd:cd05761   26 CTTSGSKPAA-DIRWFKNDKELKGVKEVQES--------GAGKTFTVTSTLRFRVDRDDDGVAVICRVDHESL 89
IgC1_MHC_Ia_HLA-F cd21023
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
125-210 1.27e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) F; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen alpha chain F (HLA-F). HLA-F, encoded by the HLA-F gene in humans, belongs to the non-classical HLA class I heavy chain paralogs. This class I molecule mainly exists as a heterodimer associated with the invariant light chain beta-2-microglobulin. HLA-F molecules can interact with both activating and inhibitory receptors on immune cells, such as NK cells, and can present a diverse panel of peptides. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409614  Cd Length: 98  Bit Score: 40.95  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 125 MKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHA 204
Cdd:cd21023   15 ISDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTELVETRPAG------DGTFQKWAAVVVPPGEEQR---YTCHVQHE 85

                 ....*.
gi 767965830 205 SLHTPL 210
Cdd:cd21023   86 GLPQPL 91
IgV_1_PVR_like cd05718
First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 ...
11-110 1.42e-04

First immunoglobulin variable (IgV) domain of poliovirus receptor (PVR, also known as CD155 and necl-5), and similar domains; The members here are composed of the first immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (necl-5)). Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), that result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted; CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" with a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the first Ig-like domain of nectin-1 (also known as poliovirus receptor related protein(PVRL)1; CD111), nectin-3 (also known as PVRL 3), nectin-4 (also known as PVRL4; LNIR receptor)and DNAX accessory molecule 1 (DNAM-1; CD226).


Pssm-ID: 409383  Cd Length: 113  Bit Score: 40.89  E-value: 1.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  11 LNDNVTIFCNIFYSQPLNITSmgITWFWKSLTFDKEVKVFE------FFGDHQEAFRpgaIVSPwRLKSGDASLRLPGIQ 84
Cdd:cd05718   13 LGGSVTLPCSLTSPGTTKITQ--VTWMKIGAGSSQNVAVFHpqygpsVPNPYAERVE---FLAA-RLGLRNATLRIRNLR 86
                         90       100
                 ....*....|....*....|....*..
gi 767965830  85 LEEAGEYRCEVVVTPL-KAQGTVQLEV 110
Cdd:cd05718   87 VEDEGNYICEFATFPQgNRQGTTWLRV 113
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
9-111 2.02e-04

Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.


Pssm-ID: 462230  Cd Length: 109  Bit Score: 40.52  E-value: 2.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830    9 TPLNDNVTIFCniFYSQPLNITSMGITWFWKSLTFDKEVKVFEFfGDHQEAFRPGAIVSpWR--LKSGDASLRLPGIQLE 86
Cdd:pfam07686   8 VALGGSVTLPC--TYSSSMSEASTSVYWYRQPPGKGPTFLIAYY-SNGSEEGVKKGRFS-GRgdPSNGDGSLTIQNLTLS 83
                          90       100
                  ....*....|....*....|....*.
gi 767965830   87 EAGEYRCEVVVTP-LKAQGTVQLEVV 111
Cdd:pfam07686  84 DSGTYTCAVIPSGeGVFGKGTRLTVL 109
IgC1_MHC_II_alpha cd05767
Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of ...
134-211 3.14e-04

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) domain of the major histocompatibility complex (MHC) class II alpha chain. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are also expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409424  Cd Length: 95  Bit Score: 39.60  E-value: 3.14e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTqkfpHPIE--ISEDVITGptikNMDGTFNVTSCLKLNSSQEDpgtVYQCVVRHASLHTPLR 211
Cdd:cd05767   23 CFVDNFFPPVINVTWLRNG----QPVTdgVSETVFLP----REDHSFRKFSYLPFTPSEGD---IYDCRVEHWGLEEPLL 91
IgC1_MHC_Ib_HLA-E cd21024
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
125-210 4.29e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) E. HLA-E is the first human class Ib major histocompatibility complex molecule to be crystallized. Like other MHC class I molecules, HLA-E is a heterodimer consisting of an a heavy chain and light chain beta-2-microglobulin. HLA-E is highly conserved and almost nonpolymorphic, and has recently been shown to be the first specialized ligand for natural killer cell receptors. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409615  Cd Length: 95  Bit Score: 39.39  E-value: 4.29e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 125 MKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDpgtVYQCVVRHA 204
Cdd:cd21024   15 ISDHEATLRCWALGFYPAEITLTWQQDGEGHTQDTELVETRPAG------DGTFQKWAAVVVPSGEEQ---RYTCHVQHE 85

                 ....*.
gi 767965830 205 SLHTPL 210
Cdd:cd21024   86 GLPEPV 91
IgV_B7-H4 cd20984
Immunoglobulin Variable (IgV) domain of B7-H4; The members here are composed of the ...
11-110 6.53e-04

Immunoglobulin Variable (IgV) domain of B7-H4; The members here are composed of the immunoglobulin variable (IgV) domain of B7-H4 (also known as B7-S1, B7x, or Vtcn1). B7-H4 is one of the B7 family of immune-regulatory ligands that act as negative regulators of T cell function; it contains one IgV domain and one IgC domain. The B7-family consists of structurally related cell-surface protein ligands, which bind to receptors on lymphocytes that regulate immune responses. The binding of B7-H4 to unidentified receptors results in the inhibition of TCR-mediated T cell proliferation, cell-cycle progression and IL-2 production. As a co-inhibitory molecule, B7-H4 is widely expressed in tumor tissues and its expression is significantly associated with poor prognosis in human cancers such as glioma, pancreatic cancer, oral squamous cell carcinoma, renal cell carcinoma, and lung cancer.


Pssm-ID: 409576  Cd Length: 110  Bit Score: 39.12  E-value: 6.53e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  11 LNDNVTIFCNifYSQPLNITSMGITWFWKSltfDKEVkVFEF------FGDHQEAFRPGAIVSPWRLKSGDASLRLPGIQ 84
Cdd:cd20984   11 IGEDGILSCT--FTPDIKLSDIVIQWLKEG---DSGL-VHEFkegkdeLSRQSPMFRGRTSLFADQVHVGNASLRLKNVQ 84
                         90       100
                 ....*....|....*....|....*.
gi 767965830  85 LEEAGEYRCEVVVTplKAQGTVQLEV 110
Cdd:cd20984   85 LTDAGTYLCIISNS--KGTGNANMEY 108
IgC1_MHC_1b_Qa-1b cd21820
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the ...
127-210 6.67e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of Qa-1b; member of the C1-set of Ig superfamily (IgSF) domains; The non-classical mouse MHC class I (MHC-I) molecule Qa-1b is a non-polymorphic MHC molecule with an important function in innate immunity. It binds and presents signal peptides of classical MHC-I molecules at the cell surface and, as such, act as an indirect sensor for the normal expression of MHC-I molecules. This signal peptide dominantly accommodated in the groove of Qa-1b is called Qdm, for Qa-1 determinant modifier, and its amino acid sequence AMAPRTLLL is highly conserved among mammalian species. The Qdm/Qa-1b complex serves as a ligand for the germ-line encoded heterodimeric CD94/NKG2A receptors expressed on natural killer (NK) cells and activated CD8+ T cells and transduces inhibitory signals to these lymphocytes. Thus, upon binding, Qa-1b signals NK cells not to engage in cell lysis. The molecular basis of Qa-1b function is unclear.


Pssm-ID: 409625  Cd Length: 98  Bit Score: 38.98  E-value: 6.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 127 ENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDpgtVYQCVVRHASL 206
Cdd:cd21820   17 EDEVTLRCWALGFYPADITLTWQLNGEELTQDMELVETRPAG------DGTFQKWAAVVVPLGKEQ---YYTCHVYHEGL 87

                 ....
gi 767965830 207 HTPL 210
Cdd:cd21820   88 PEPL 91
IgV_CAR_like cd20960
Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and ...
13-108 6.76e-04

Immunoglobulin Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins; The members here are composed of the Variable (V) domain of the Coxsackievirus and Adenovirus Receptor (CAR), and similar proteins. CAR, which is encoded by human CXADR gene, is a cell adhesion molecule of the Immunoglobulin (Ig) superfamily. The CAR acts as a type I membrane receptor for group B1-B6 coxsackie viruses and subgroup C adenoviruses. For instance, adenovirus interacts with the coxsackievirus and adenovirus receptor to enter epithelial airway cells. The CAR is also shown to be involved in physiological processes such as neuronal and heart development, epithelial tight junction integrity, and tumor suppression. The CAR is a component of the epithelial apical junction complex that may function as a homophilic cell adhesion molecule and is essential for tight junction integrity. The CAR is also involved in transepithelial migration of leukocytes through adhesive interactions with JAML a transmembrane protein of the plasma membrane of leukocytes. The interaction between both receptors also mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. The CAR is composed of one V-set and one C2-set Ig module, a single transmembrane helix, and an intracellular domain. This group belongs to the V-set of IgSF domains, having A, B, E and D strands in one beta-sheet and A', G, F, C, C' and C" in the other


Pssm-ID: 409552  Cd Length: 114  Bit Score: 39.36  E-value: 6.76e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  13 DNVTIFCNiFYSQPLNITSMGITWFwkSLTFDKEVKV-FEFFGDH-QEAFRPG-----AIVSPWrlKSGDASLRLPGIQL 85
Cdd:cd20960   16 ENVTLPCH-HQLGLEDQGTLDIEWL--LLPSDKVEKVvITYSGDRvYNHYYPAlkgrvAFTSND--LSGDASLNISNLKL 90
                         90       100
                 ....*....|....*....|...
gi 767965830  86 EEAGEYRCEVVVTPLKAQGTVQL 108
Cdd:cd20960   91 SDTGTYQCKVKKAPGYAWSKITL 113
IgC1_MHC_Ia_HLA-G cd21022
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
129-210 8.50e-04

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) G. HLA-G histocompatibility antigen (also known as human leukocyte antigen G ; HLA-G) is a protein that in humans is encoded by the HLA-G gene. HLA-G belongs to the HLA nonclassical class I heavy chain paralogs. This class I molecule is a heterodimer consisting of a heavy chain and light chain, beta-2-microglobulin. The heavy chain is anchored in the membrane. HLA-G may play a role in immune tolerance in pregnancy, being expressed in the placenta by extravillous trophoblast cells (EVT), while the classical MHC class I genes (HLA-A and HLA-B) are not. Immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class I and class II. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells. MHC class II molecules play a key role in the initiation of the antigen-specific immune repose. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409613  Cd Length: 94  Bit Score: 38.59  E-value: 8.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 129 EDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHASLHT 208
Cdd:cd21022   18 EATLRCWALGFYPAEIILTWQRDGEDQTQDVELVETRPAG------DGTFQKWAAVVVPSGEEQR---YTCHVQHEGLPE 88

                 ..
gi 767965830 209 PL 210
Cdd:cd21022   89 PL 90
IgC1_MHC_II_beta_I-E cd20998
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of ...
127-210 1.09e-03

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) I-E. Three genetically distinct isotypes of class II MHC molecules are found in humans (HLA-DR, HLA-DQ, and HLA-DP), and two in mice (I-E and I-A). I-A and I-E molecules have the same basic features insofar as peptide loading and presentation, although each interacts with distinctly different sets of peptides. They also differ in that there is a relatively high incidence of deletion of the I-E gene in both inbred strains of mice as well as wild mice and the lack of the reverse situation i.e. the deletion of I-A genes. A detailed structural understanding of the similarities and differences between I-A and the paralogous I-E could help illuminate the respective roles these molecules play in peptide presentation and T cell activation. Mouse I-Ag7 has a genetic susceptibility to autoimmune diabetes due to its small, uncharged amino acid residue at position 57 of their beta chain which results in the absence of a salt bridge between beta 57 and Arg alpha 76, which is adjacent to the P9 pocket of the peptide-binding groove. MHC class II molecules play a key role in the initiation of the antigen-specific immune reponse. These molecules have been shown to be expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice. The expression of these molecules has been shown to be induced in nonprofessional APCs such as keratinocyctes, and they are expressed on the surface of activated human T cells and on T cells from other species. The MHC II molecules present antigenic peptides to CD4(+) T-lymphocytes. These peptides derive mostly from proteolytic processing via the endocytic pathway, of antigens internalized by the APC. These peptides bind to the MHC class II molecules in the endosome before they are transported to the cell surface. MHC class II molecules are heterodimers, comprised of two similarly-sized membrane-spanning chains, alpha and beta. Each chain had two globular domains (N- and C-terminal), and a membrane-anchoring transmembrane segment. The two chains form a compact four-domain structure. The peptide-binding site is a cleft in the structure.


Pssm-ID: 409590  Cd Length: 99  Bit Score: 38.21  E-value: 1.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 127 ENEDKYMCESSGFYPEAINITWekqtqkFPHPIEISEDVITGPTIKNMDGTFNVTSCLKlnsSQEDPGTVYQCVVRHASL 206
Cdd:cd20998   20 EHHNLLVCSVSDFYPGNIEVRW------FRNGKEEKTGIVSTGLVRNGDWTFQTLVMLE---TVPQSGEVYTCQVEHPSL 90

                 ....
gi 767965830 207 HTPL 210
Cdd:cd20998   91 TDPV 94
IgC1_TCR_beta cd05769
T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig ...
134-203 1.16e-03

T cell receptor (TCR) beta chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the T cell receptor (TCR) beta chain constant immunoglobulin domain. TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the beta chain. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The antigen binding site is formed by the variable domains of the alpha and beta chains, located at the N-terminus of each chain. Alpha/beta TCRs recognize antigens differently from gamma/delta TCRs.


Pssm-ID: 409426 [Multi-domain]  Cd Length: 116  Bit Score: 38.51  E-value: 1.16e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpiEISEDVITGP-TIKNMDGTFNVTSCLKLNSSQ-EDPGTVYQCVVRH 203
Cdd:cd05769   25 CLATGFYPDHVSLSWKVNGK------EVKDGVATDPqALRENTSTYSLSSRLRVSATEwFNPRNTFTCIVKF 90
IgC1_CH3_IgAEM_CH2_IgG cd07696
CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, ...
142-210 1.26e-03

CH3 domain (third constant Ig domain of heavy chains) in immunoglobulin heavy alpha, epsilon, and mu chains, and CH2 domain (second constant Ig domain of the gheavy chain) in immunoglobulin heavy gamma chain; member of the C1-set of Ig superfamily (IgSF) ; The members here are composed of the third immunoglobulin constant domain (IgC) of the gamma heavy chains and the second immunoglobulin constant domain (IgC) of alpha, epsilon, and mu heavy chains. This domain is found on the Fc fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns.


Pssm-ID: 409493  Cd Length: 98  Bit Score: 37.82  E-value: 1.26e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767965830 142 EAINITWEKQTQKfphpieiSEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTPL 210
Cdd:cd07696   32 EEVNVTWSREDGN-------EVLASTTNPEKHYNATLSVVSTLTVCADDWDNGKTFKCKVTHPDLPSPI 93
IgC1_MHC_Ia_HLA-A cd21027
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
124-210 1.46e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) A. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-A gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. HLA-A2 is associated with spontaneous abortions, HIV, and Hodgkin lymphoma. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409618  Cd Length: 95  Bit Score: 37.89  E-value: 1.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 124 GMKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRH 203
Cdd:cd21027   14 AVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAG------DGTFQKWAAVVVPSGQEQR---YTCHVQH 84

                 ....*..
gi 767965830 204 ASLHTPL 210
Cdd:cd21027   85 EGLPKPL 91
IgI_2_Necl-3 cd05884
Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set ...
134-206 1.57e-03

Second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3); member of the I-set of Ig superfamily domains; The members here are composed of the second immunoglobulin (Ig)-like domain of nectin-like molecule-3 (Necl-3; also known as cell adhesion molecule 2 (CADM2)). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 through Necl-5). These have an extracellular region containing three Ig-like domains, one transmembrane region, and one cytoplasmic region. Necl-3 has been shown to accumulate in tissues of the central and peripheral nervous system where it is expressed in ependymal cells and myelinated axons. It is observed at the interface between the axon shaft and the myelin sheath. Ig domains are likely to participate in ligand binding and recognition.


Pssm-ID: 409467  Cd Length: 104  Bit Score: 37.99  E-value: 1.57e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767965830 134 CESSGFYPEAiNITWEKQTQKFPHPIEISEDVITGPTiknmdgtFNVTSCLKLNSSQEDPGTVYQCVVRHASL 206
Cdd:cd05884   27 CKTSGSKPAA-DIRWFKNDKEVKDVKYLKAEDANRKT-------FTVSSSLDFHVDRDDDGVAITCRVDHESL 91
IgV_PDl1 cd20947
Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here ...
14-93 1.72e-03

Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here are composed of the immunoglobulin variable (IgV) domain of Programmed death ligand 1 (PD-L1; also known as Cluster of Differentiation 274 (CD274)). PD-L1 is a cell-surface ligand that competes with PD-L2 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. Like PD-L2, PD-L1 interacts with PD-1 and suppresses T cell proliferation and cytokine production. The PD-1 receptor is expressed on the surface of activated T cells, while PD-L1 is expressed on cancer cells. When PD-1 and PD-L1 bind together, they form a molecular shield protecting tumor cells from being destroyed by the immune system. Thus, inhibiting the binding of PD-L1 to PD-1 with an antibody leads to killing of tumor cells by T cells. PD-1 inhibitors (such as Pembrolizumab, Nivolumab, and Cemiplimab) and PD-L1 inhibitors (such as Atezolizumab, Avelumab, and Durvalumab ) are an emerging class of immunotherapy that stimulate lymphocytes against tumor cells.


Pssm-ID: 409539  Cd Length: 110  Bit Score: 37.99  E-value: 1.72e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  14 NVTIFCNIFYSQPLNITSMGITWFWKsltfDKEVKVF----EFFGDHQEAFRPGAIVSPWRLKSGDASLRLPGIQLEEAG 89
Cdd:cd20947   15 NMTIECKFPVEKQLDLAALIVYWEME----DKNIIQFvhgeEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAG 90

                 ....
gi 767965830  90 EYRC 93
Cdd:cd20947   91 VYRC 94
C2-set_2 pfam08205
CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.
134-209 1.78e-03

CD80-like C2-set immunoglobulin domain; These domains belong to the immunoglobulin superfamily.


Pssm-ID: 400489  Cd Length: 89  Bit Score: 37.40  E-value: 1.78e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767965830  134 CESSGFYPEAiNITWEKQTQkfPHpieisEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTP 209
Cdd:pfam08205  21 CSSAGGKPAP-RITWYLDGK--PL-----EAAETSSEQDPESGLVTVTSELKLVPSRSDHGQSLTCQVSYGALRGS 88
IgC1_TCR_gamma cd07697
T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig ...
126-203 2.07e-03

T cell receptor (TCR) gamma chain constant immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) constant (C) domain of the gamma chain of gamma-delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha-beta TCRs, but a small subset contain gamma-delta TCRs. Alpha-beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma-delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing and MHC independently of the bound peptide. Gamma-delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds.


Pssm-ID: 409494  Cd Length: 98  Bit Score: 37.24  E-value: 2.07e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 767965830 126 KENEDKYMCESSGFYPEAINITWEKQTQKFphPIEISEdvitGPTIKNMDgTFNVTSCLKLnsSQEDPGTVYQCVVRH 203
Cdd:cd07697   16 KQKAGTYLCLLENFFPDVIKIHWREKKSDT--ILESQE----GNTEKTKD-TYMKFSWLTV--PKKSLGKEHRCIYKH 84
IgC1_MHC_Ib_HLA-Cw3-4 cd21025
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; ...
125-210 2.23e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of HLA-Cw3 and HLA-Cw4. HLA-C belongs to the MHC class I heavy chain receptors. The C receptor is a heterodimer consisting of a HLA-C mature gene product and beta-2-microglobulin. The mature C chain is anchored in the membrane. MHC Class I molecules, like HLA-C, are expressed in nearly all cells, and present small peptides to the immune system which surveys for non-self peptides. HLA-C is a locus on chromosome 6, which encodes for a large number of HLA-C alleles that are Class-I MHC receptors. Class Ib histocompatibility leukocyte antigens (HLA)-Cw3 and (HLA)-Cw4 are ligands for the natural killer (NK) cell inhibitory receptors KIR2DL2 and KIR2DL1, respectively. HLA-Cw3 and related alleles (HLA-Cw1, -Cw7, and -Cw8) contain Ser77 and Asn80 and interact with KIR that are reactive with the GL183 antibody Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. HLA-Cw4 and related alleles (HLA-Cw2, -Cw5, and -Cw6) have Asn77 and Lys80 and are recognized by KIR reactive with the EB6 15 or HP-3E4 16 antibody. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409616  Cd Length: 96  Bit Score: 37.48  E-value: 2.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 125 MKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHA 204
Cdd:cd21025   15 VSDHEATLRCWALGFYPAEITLTWQWDGEDQTQDTELVETRPAG------DGTFQKWAAVVVPSGEEQR---YTCHVQHE 85

                 ....*.
gi 767965830 205 SLHTPL 210
Cdd:cd21025   86 GLPEPL 91
IgC1_beta2m cd05770
Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of ...
134-209 2.84e-03

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.


Pssm-ID: 409427  Cd Length: 94  Bit Score: 37.07  E-value: 2.84e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 767965830 134 CESSGFYPEAINITWEKQTQKfphpieiSEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPgtvYQCVVRHASLHTP 209
Cdd:cd05770   23 CYVSGFHPPDIEIRLLKNGVK-------IEDVEQSDLSFSKDWTFYLLKYTEFTPTKGDE---YACRVRHNTLSEP 88
Ig_CSPGs_LP_like cd05714
Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage ...
11-110 3.25e-03

Immunoglobulin (Ig)-like domain of chondroitin sulfate proteoglycans (CSPGs), human cartilage link protein (LP), and similar domains; The members here are composed of the immunoglobulin (Ig)-like domain similar to that found in chondroitin sulfate proteoglycans (CSPGs) and human cartilage link protein (LP). Included in this group are the CSPGs aggrecan, versican, and neurocan. In CSPGs, this Ig-like domain is followed by hyaluronan (HA)-binding tandem repeats, and a C-terminal region with epidermal growth factor-like, lectin-like, and complement regulatory protein-like domains. Separating these N- and C-terminal regions is a nonhomologous glycosaminoglycan attachment region. In cartilage, aggrecan forms cartilage link protein stabilized aggregates with hyaluronan (HA). These aggregates contribute to the tissue's load bearing properties. Aggrecan and versican have a wide distribution in connective tissue and extracellular matrices. Neurocan is localized almost exclusively in nervous tissue. Aggregates having other CSPGs substituting for aggrecan may contribute to the structural integrity of many different tissues. There is considerable evidence that HA-binding CSPGs are involved in developmental processes in the central nervous system. Members of the vertebrate HPLN (hyaluronan/HA and proteoglycan binding link) protein family are physically linked adjacent to CSPG genes.


Pssm-ID: 409379  Cd Length: 123  Bit Score: 37.57  E-value: 3.25e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830  11 LNDNVTIFCNiFYSQP--LNITSMGITWFWKSLTFD----KEVKVFEFFGD---HQEAFRPGAIVSPWRLKSGDASLRLP 81
Cdd:cd05714   11 LGGNVTLPCK-FYRDPtaFGSGIHKIRIKWTKLTSDsgylKEVDVLVAMGNvvyHKKTYGGRVSVPLKPGSDSDASLVIT 89
                         90       100
                 ....*....|....*....|....*....
gi 767965830  82 GIQLEEAGEYRCEVVVTPLKAQGTVQLEV 110
Cdd:cd05714   90 DLTASDYGLYRCEVIEGIEDDQDVVALDV 118
IgC1_MHC_Ia_HLA-B cd21026
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
125-210 3.41e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) B and similar proteins. The classical class I molecules (HLA-A, -B, and -C) are responsible for the presentation of endogenous antigen to CD8+ T cells. The receptor is a heterodimer, and is composed of a heavy alpha chain and smaller beta chain. The alpha chain is encoded by a variant HLA-B gene, and the beta chain (beta-2-microglobulin) is an invariant beta-2-microglobulin molecule. The beta-2-microglobulin protein is coded for by a separate region of the human genome. Human leukocyte antigen (HLA) B*3501 (B35) is a common human allele involved in mediating protective immunity against HIV. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409617  Cd Length: 97  Bit Score: 36.72  E-value: 3.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 125 MKENEDKYMCESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHA 204
Cdd:cd21026   15 ISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAG------DRTFQKWAAVVVPSGEEQR---YTCHVQHE 85

                 ....*.
gi 767965830 205 SLHTPL 210
Cdd:cd21026   86 GLPKPL 91
IgC1_2_PVR_like cd05719
Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and Necl-5), ...
134-217 3.42e-03

Second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and Necl-5), and similar domains; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second immunoglobulin (Ig) domain of poliovirus receptor (PVR, also known as CD155 and nectin-like protein 5 (Necl-5)) and similar proteins. Poliovirus (PV) binds to its cellular receptor (PVR/CD155) to initiate infection. CD155 is a membrane-anchored, single-span glycoprotein; its extracellular region has three Ig-like domains. There are four different isotypes of CD155 (referred to as alpha, beta, gamma, and delta), these result from alternate splicing of the CD155 mRNA, and have identical extracellular domains. CD155-beta and CD155-gamma are secreted, while CD155-alpha and CD155-delta are membrane-bound and function as PV receptors. The virus recognition site is contained in the amino-terminal domain, D1. Having the virus attachment site on the receptor distal from the plasma membrane may be important for successful initiation of infection of cells by the virus. CD155 binds in the poliovirus "canyon" and has a footprint similar to that of the intercellular adhesion molecule-1 receptor on human rhinoviruses. This group also includes the second Ig-like domain of nectin-1, also known as poliovirus receptor related protein(PVRL)1 or CD111.


Pssm-ID: 409384  Cd Length: 96  Bit Score: 36.70  E-value: 3.42e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAiNITWE---KQTQKFPhpieisedvitgpTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRHASLHTPL 210
Cdd:cd05719   23 CISANGKPPA-SVTWEtdlKGEASTT-------------QVRGSNGTVTVTSRYRLVPSREADGQPLTCVVEHPSLEKDQ 88

                 ....*..
gi 767965830 211 RSNFTLT 217
Cdd:cd05719   89 RISVTLN 95
IgC1_MHC_Ia_H2Db_H2Ld cd21018
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte ...
134-210 4.40e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen (HLA) H2Db and H2Ld. H-2Ld complexed with peptide QL9 (or p2Ca) and complexed with influenza virus peptide NP366-374 (ASNEN-METM), respectively are high-affinity alloantigens for the 2C T cell receptor (TCR). The a1-a2 super domains of H-2Ld, H-2Db, and H-2Kb closely superimpose. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409609  Cd Length: 95  Bit Score: 36.26  E-value: 4.40e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767965830 134 CESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHASLHTPL 210
Cdd:cd21018   24 CWALGFYPADITLTWQLNGEELTQDMELVETRPAG------DGTFQKWASVVVPLGKEQN---YTCRVYHEGLPEPL 91
IgC1_MHC_Ia_H-2Kb cd21019
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the ...
129-210 5.15e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H-2Kb. H-2Kb is an alloantigen for the 2C T cell receptor (TCR). H-2Kb forms a complex with beta-2-microglobulin, and a peptide, including VSV-8 (RGYVYNGL), SEV-9 (FAPGNYPAL), and OVA-8 (SIINFEKL). Comparison of the OVA-8, VSV-8, and SEV-9 complexes with H-2Kb indicates that four side chains (Lys-66, Glu-152, Arg-155, and Trp-167) adopt peptide-specific conformations. H-2Kb paralogs include H-2Db, H-2Kbml and H-2KbI1s. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409610  Cd Length: 94  Bit Score: 36.24  E-value: 5.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 129 EDKYM--CESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDpgtVYQCVVRHASL 206
Cdd:cd21019   16 EDKVTlrCWALGFYPADITLTWQLNGEELIQDMELVETRPAG------DGTFQKWASVVVPLGKEQ---YYTCHVYHQGL 86

                 ....
gi 767965830 207 HTPL 210
Cdd:cd21019   87 PEPL 90
IgC1_MHC_Ia_H-2Dd cd21020
Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the ...
134-210 6.36e-03

Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ia major histocompatibility complex (MHC) immunoglobulin domain of H2-Dd. Mouse MHC is composed of 11 subclasses. It includes the classical MHC class I (MHC-Ia) that comprises H-2D, H-2K and H-2L subclasses, the non-classical MHC class I (MHCIb) that comprises H-2Q, H-2M and H-2T subclasses, the classical MHC class II (MHC-IIa) that includes H-2A(I-A) and H-2E(I-E) subclasses, and the non-classical MHC class II (MHC-IIb) comprises H-2M and H-2O. H-2K, H-2D, and H-2L are 80 to 90% homologous at the amino acid level yet appear to be involved in different recognition reactions and are differentially expressed on lymphoid cells. Class I MHC proteins bind antigenic peptide fragments and present them to CD8+ T lymphocytes. Class I molecules consist of a transmembrane alpha chain and a small chain called the beta-2-microglobulin. The alpha chain contains three extracellular domains, two of which fold together to form the peptide-binding cleft (alpha1 and alpha2), and one which has an Ig fold (alpha3). Peptide binding to class I molecules occurs in the endoplasmic reticulum (ER) and involves both chaperones and dedicated factors to assist in peptide loading. Class I MHC molecules are expressed on most nucleated cells.


Pssm-ID: 409611  Cd Length: 95  Bit Score: 35.89  E-value: 6.36e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767965830 134 CESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFN--VTSCLKLNSSQEdpgtvYQCVVRHASLHTPL 210
Cdd:cd21020   24 CWALGFYPADITLTWQLNGEELTQEMELVETRPAG------DGTFQkwASVVVPLGKEQK-----YTCHVEHEGLPEPL 91
IgC1_MHC_Ib_T10_T22_like cd21016
Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar ...
134-210 8.14e-03

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of T10, T22, and similar proteins; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of the murine H-2T-encoded T10, T22, and similar proteins. T10 and T22 are highly related nonclassical major histocompatibility complex (MHC) class Ib proteins that bind to certain gammadelta T cell receptors (TCRs) in the absence of other components. Classical MHC class I (class Ia) molecules participate in immune responses by presenting peptide antigens to cytolytic alpha beta T cells. Many nonclassical MHC class I (class Ib) molecules have distinct antigen-binding capabilities, suggesting that they have evolved for specific tasks that are distinct from those of MHC class Ia. Members of the IgC family are components of immunoglobulin, T-cell receptors, CD1 cell surface glycoproteins, secretory glycoproteins A/C, and major histocompatibility complex (MHC) class I/II molecules. In immunoglobulins, each chain is composed of one variable domain (IgV) and one or more IgC domains. These names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. The IgV domain is responsible for antigen binding, and the IgC domain is involved in oligomerization and molecular interactions.


Pssm-ID: 409607  Cd Length: 97  Bit Score: 35.85  E-value: 8.14e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 767965830 134 CESSGFYPEAINITWEKQTQKFPHPIEISEDVITGptiknmDGTFNVTSCLKLNSSQEDPgtvYQCVVRHASLHTPL 210
Cdd:cd21016   24 CWALGFYPADITLTWQKDGEELTQDMEFVETRPAG------DGTFQKWAAVVVPLGKEQS---YTCHVYHEGLPEPL 91
IgC1_CH1_IgA cd21818
CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; ...
134-203 9.90e-03

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy alpha chain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the first immunoglobulin constant-1 set domain of alpha chains. It belongs to a family composed of the first immunoglobulin constant-1 set domain of alpha, epsilon, gamma, and mu heavy chains. This domain is found on the Fab antigen-binding fragment. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda; each is composed of a constant domain and a variable domain. There are five types of heavy chains: alpha, delta, epsilon, gamma, and mu, all consisting of a variable domain (VH) with three (alpha, delta and gamma) or four (epsilon and mu) constant domains (CH1 to CH4). Ig molecules are modular proteins, in which the variable and constant domains have clear, conserved sequence patterns. This group belongs to the C1-set of IgSF domains, which are classical Ig-like domains resembling the antibody constant domain. C1-set domains are found almost exclusively in molecules involved in the immune system, such as in immunoglobulin light and heavy chains, in the major histocompatibility complex (MHC) class I and II complex molecules, and in various T-cell receptors.


Pssm-ID: 409623  Cd Length: 94  Bit Score: 35.17  E-value: 9.90e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767965830 134 CESSGFYPEAINITWEKQTQkfphpieiSEDVITGPTIKNMDGTFNVTSCLKLNSSQEDPGTVYQCVVRH 203
Cdd:cd21818   22 CLVQGFFPEPVNVTWNYSGK--------GGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEAYKCSVQH 83
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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