Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        2 IQMTQSPSSLSASVGDRVTITCRASQ-VIRRSLAWYQQKPGKAPKLLIYAASNLASGVPSRFSGSGSGTDFTLTISSLQP 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQsISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
2FJH_L       81 EDFATYYCQQSNTSPLTFGQGTKVEI 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        2 IQMTQSPSSLSASVGDRVTITCRASQ-VIRRSLAWYQQKPGKAPKLLIYAASNLASGVPSRFSGSGSGTDFTLTISSLQP 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQsISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
2FJH_L       81 EDFATYYCQQSNTSPLTFGQGTKVEI 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        115 VFIFPPSDEQLKsGTASVVCLLNNFYPREAKVQWKVDNALQSgNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYAC 194
Cdd:pfam07654   1 VYVFPPSPEELG-KPNTLTCLVTGFYPPDITVTWLKNGQEVT-EGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78

                  ....*..
2FJH_L        195 EVTHQGL 201
Cdd:pfam07654  79 RVEHEGL 85

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L           8 PSSLSASVGDRVTITCRASQVIRRSLAWYQQKPgkapKLLIYaasnlasgvPSRFSGSGSGTDFTLTISSLQPEDFATYY 87
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                           90
                   ....*....|....*....
2FJH_L          88 CQQSNTSPLTFGqGTKVEI 106
Cdd:smart00410  68 CAATNSSGSASS-GTTLTV 85

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. 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 composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        2 IQMTQSPSSLSASVGDRVTITCRASQ-VIRRSLAWYQQKPGKAPKLLIYAASNLASGVPSRFSGSGSGTDFTLTISSLQP 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQsISSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
2FJH_L       81 EDFATYYCQQSNTSPLTFGQGTKVEI 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. 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 composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: 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. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        4 MTQsPSSLSASVGDRVTITCRASQVIRRS--LAWYQQKPGKAPKLLIYAASNLASGVPSRFSGSGSGTDFTLTISSLQPE 81
Cdd:cd04984   2 LTQ-PSSLSVSPGETVTITCTGSSGNISGnyVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTE 80

                        90       100
                ....*....|....*....|...
2FJH_L       82 DFATYYCQQSNTSPLTFGQGTKV 104
Cdd:cd04984  81 DEADYYCQVWDSNSYVFGGGTKL 103

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'.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      114 SVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESvTEQDSKDSTYSLSSTLTLSKADYEKHKVYA 193
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTS-SPVEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                        90
                ....*....|....*.
2FJH_L      194 CEVTHQGLSSPVTKSF 209
Cdd:cd00098  80 CVVTHESLKSPLSKTW 95

Immunoglobulin C-Type;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
2FJH_L         129 TASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSkDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSP 204
Cdd:smart00407   1 KATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNS-DGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPSDEQL-KSGTASVVCLLNNFYPREAKVQWKVDN-ALQSGNSQESVTEQDSkDSTYSLSSTLTLSKADYEKHK 190
Cdd:cd05768   1 PSVYLLPPPEEELsLNETVTLTCLVKGFYPEDIFVSWLQNGePLPSADYKTTAPVPES-DGSFFVYSKLNVSTADWNSGD 79

                        90       100
                ....*....|....*....|..
2FJH_L      191 VYACEVTHQGLSSPVT-KSFNR 211
Cdd:cd05768  80 VFSCVVGHEALPLQFTqKSIDK 101

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L           8 PSSLSASVGDRVTITCRASQVIRRSLAWYQQKPgkapKLLIYaasnlasgvPSRFSGSGSGTDFTLTISSLQPEDFATYY 87
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGTYT 67

                           90
                   ....*....|....*....
2FJH_L          88 CQQSNTSPLTFGqGTKVEI 106
Cdd:smart00410  68 CAATNSSGSASS-GTTLTV 85

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      112 APSVFIFPPS-DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQ-ESVTEQDSkDSTYSLSSTLTLSKADYEK- 188
Cdd:cd05769   2 PPTVALFPPSeAEIRNKRKATLVCLATGFYPDHVSLSWKVNGKEVKDGVAtDPQALREN-TSTYSLSSRLRVSATEWFNp 80

                        90       100
                ....*....|....*....|....*
2FJH_L      189 HKVYACEVTHQGLSSpvTKSFNRGE 213
Cdd:cd05769  81 RNTFTCIVKFYGGTD--TDTWTQGI 103

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) delta chain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the delta 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. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        3 QMTQSPSSLSASVGDRVTITCRASQVIRR-SLAWYQQKPGKAPKLLIYAASNLASGVPSRFSGSGSGTD--FTLTISSLQ 79
Cdd:cd07706   1 KVTQAQPDVSVQVGEEVTLNCRYETSWTNyYLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksISLTISALQ 80

                        90       100       110
                ....*....|....*....|....*....|
2FJH_L       80 PEDFATYYCQQS---NTSPLTFGQGTKVEI 106
Cdd:cd07706  81 LEDSAKYFCALSlpyDTDKLIFGKGTRLTV 110

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPS-DEQLKSGTASVVCLLNNFYPREAKVQW-KVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHK 190
Cdd:cd16093   2 PTVSLHAPSrEEFLGNRTATFVCLATGFSPKTISFKWlRNGKEVTSSTGAVVEEPKEDGKTLYSATSFLTITESEWKSQT 81

                        90
                ....*....|.
2FJH_L      191 VYACEVTHQGL 201
Cdd:cd16093  82 EFTCEFKHKGE 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPSDEQL-KSGTASVVCLLNNFYPREA-KVQWKVdnalQSGNSQESVTEQDSK--DSTYSLSSTLTLSKADYEK 188
Cdd:cd07696   1 VSVFLIPPSPKDLfLTKSAKVTCLVVDLTSIEEvNVTWSR----EDGNEVLASTTNPEKhyNATLSVVSTLTVCADDWDN 76

                        90       100
                ....*....|....*....|
2FJH_L      189 HKVYACEVTHQGLSSPVTKS 208
Cdd:cd07696  77 GKTFKCKVTHPDLPSPIVKS 96

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'.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      112 APSVFIF---PPSDEQLKsgtasVVCLLNNFYPREAKVQWKVDNALQSgNSQESVTEQDSKDSTYSLSSTLTLSKADyeK 188
Cdd:cd21029   2 KPRVRLSsrpSPGDGHLQ-----LSCHVTGFYPRPIEVTWLRDGQEQM-DGTQSGGILPNHDGTYQLRKTLDIAPGE--G 73

                        90
                ....*....|....*...
2FJH_L      189 HKvYACEVTHQGLSSPVT 206
Cdd:cd21029  74 AG-YSCRVDHSSLKQDLI 90

Immunoglobulin (Ig)-like variable (V) domain of Cluster of Differentiation (CD) 8 alpha chain; The members here are composed of the immunoglobulin (Ig)-like variable domain of the Cluster of Differentiation (CD) 8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        7 SPSSLSASVGDRVTITCRASQVIRRSLAWYQQKPGKAPKL--LIYAASNLASGVP-----SRFSGSGSGTDFTLTISSLQ 79
Cdd:cd05720   4 SPRKRDAQLGQKVELVCEVLNSVPQGCSWLFQPRGSAPQPtfLLYLSSSNKTKWAegldsKRFSGSRSGSSYVLTLKDFR 83

                        90       100
                ....*....|....*....|....*
2FJH_L       80 PEDFATYYCQQSNTSPLTFGQGTKV 104
Cdd:cd05720  84 KEDEGYYFCSVISNSVLYFSSFVPV 108

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPSdEQLKSGTASVVCLLNNFYPREAKVQW----KVDNALQSGNSQESV-TEQDSKDSTYSLSSTLTLSKADYE 187
Cdd:cd05771   1 PRVRLSPKN-LVKPDLPQTLSCHIAGYYPLDVDVEWlreePGGSESQVSRDGVSLsSHRQSVDGTYSISSYLTLEPGTEN 79

                        90       100
                ....*....|....*....|.
2FJH_L      188 KHKVYACEVTHQGLSSPVTKS 208
Cdd:cd05771  80 RGATYTCRVTHVSLEEPLSVS 100

Immunoglobulin (Ig) variable (V) domain of Cluster of Differentiation (CD) 8 beta chain; The members here are composed of the immunoglobulin (Ig)-like domain in Cluster of Differentiation (CD) 8 beta. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation, and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alpha/alpha or alpha/beta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners, etc. Each CD8 subunit is comprised of an extracellular domain containing a V-type Ig-like domain, a single pass transmembrane portion, and a short intracellular domain. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        6 QSPSSLSASVGDRVTITCRA-SQVIRRSLAWYQQK--PGKAPKLLIYAASNLASGV-------PSRFS--GSGSGTDFTL 73
Cdd:cd07700   3 QTPGSLLVQTNQTVKMSCEAkTSPKNTRIYWLRQRqaPSKDSHFEFLASWDPSKGIvygegvdQEKLIilSDSDSSRYIL 82

                        90       100       110
                ....*....|....*....|....*....|
2FJH_L       74 TISSLQPEDFATYYCQQSNTSPLTFGQGTK 103
Cdd:cd07700  83 SLMSVKPEDSGTYFCMTVGSPELIFGTGTK 112

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPSDEQLKSgTASVVCLLNNFYPREAKVQWKVDNALQsGNSQESVTEQDSKDSTYSLSSTL--TLSKADyekhk 190
Cdd:cd05766   4 PSVKVSPTKTGPLEH-PNLLVCSVTGFYPAEIEVKWFRNGQEE-TAGVVSTELIPNGDWTFQILVMLetTPRRGD----- 76

                        90
                ....*....|....*.
2FJH_L      191 VYACEVTHQGLSSPVT 206
Cdd:cd05766  77 VYTCQVEHSSLQSPLT 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      112 APSVFIFPPSDEQL-KSGTasVVCLLNNFYPREAKVQWkvdnaLQSGnsqESVTEQDSkDSTYSLSSTLTLSKADY---- 186
Cdd:cd05767   2 PPEVTVFPKSPVELgEPNT--LICFVDNFFPPVINVTW-----LRNG---QPVTDGVS-ETVFLPREDHSFRKFSYlpft 70

                        90       100
                ....*....|....*....|..
2FJH_L      187 -EKHKVYACEVTHQGLSSPVTK 207
Cdd:cd05767  71 pSEGDIYDCRVEHWGLEEPLLK 92

Immunoglobulin (Ig)-like variable (V) domain of the Signal-Regulatory Protein (SIRP); The members here are composed of the immunoglobulin (Ig)-like domain of the Signal-Regulatory Protein (SIRP). 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 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 with much less affinity. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L        3 QMTQSPSSLSASVGDRVTITCRASQVIRRS-LAWYQqkpGKAP-KLLIYaasNLASGVPSRFSGSGSGT-----DFTLTI 75
Cdd:cd16097   1 QVIQPEKSVSVAAGESATLHCTVTSLIPVGpIQWFR---GAGPgRELIY---NQKEGHFPRVTTVSDLTkrnnmDFSIRI 74

                        90
                ....*....|...
2FJH_L       76 SSLQPEDFATYYC 88
Cdd:cd16097  75 SNITPADAGTYYC 87

First immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4; member of the V-set of IgSF domains; The members here are composed of the first immunoglobulin (Ig) domain of Cluster of Differentiation (CD) 4. CD4 and CD8 are the two primary co-receptor proteins found on the surface of T cells, and the presence of either CD4 or CD8 determines the function of the T cell. CD4 is found on helper T cells, where it is required for the binding of MHC (major histocompatibility complex) class II molecules, while CD8 is found on cytotoxic T cells, where it is required for the binding of MHC class I molecules. CD4 contains four immunoglobulin domains, with the first three included in this hierarchy. The fourth domain has a general Ig architecture, but has slight topological changes in the arrangement of beta strands relative to the other structures in this family and is not specifically included in the hierarchy.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L       16 GDRVTITCRASQVIRRSLAW---YQQKP-GKAPKLLIYAASNLASGVPSRFSGSGSGTdFTLTISSLQPEDFATYYCQQS 91
Cdd:cd07690   9 GDTAELPCTASQKKSIQFHWknsNQIKIlGNQGSFLTKGPSKLNDRADSRRNLWDQGS-FPLIIKNLKIEDSDTYICEVE 87

                .
2FJH_L       92 N 92
Cdd:cd07690  88 D 88

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      119 PPSDEQlksgtASVVCLLNNFYPREAKVQWKVDNALQSGNSqESVTEQDSKDSTYSLSSTLTLSKADYEKhkvYACEVTH 198
Cdd:cd21025  14 PVSDHE-----ATLRCWALGFYPAEITLTWQWDGEDQTQDT-ELVETRPAGDGTFQKWAAVVVPSGEEQR---YTCHVQH 84

                ....*...
2FJH_L      199 QGLSSPVT 206
Cdd:cd21025  85 EGLPEPLT 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPSDEQLKSGTAsVVCLLNNFYPREAKVQWkvdnaLQSGNSQE----SVTEQDSKDSTYSlssTLTLSKADYEK 188
Cdd:cd21000   4 PKVTVYPAKTQPLQHHNL-LVCSVNGFYPGSIEVRW-----FRNGQEEKagvvSTGLIQNGDWTFQ---TLVMLETVPRS 74

                        90
                ....*....|....*...
2FJH_L      189 HKVYACEVTHQGLSSPVT 206
Cdd:cd21000  75 GEVYTCQVEHPSVTSPLT 92

Immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin domain of Zn-alpha2-glycoprotein (ZAG). ZAG is a soluble protein that is present in serum and other body fluids. ZAG stimulates lipid degradation in adipocytes and causes the extensive fat losses associated with some advanced cancers. The 2.8 angstrom crystal structure of ZAG resembles a class I major histocompatibility complex (MHC) heavy chain, but ZAG does not bind the class I light chain beta-2-microglobulin. The ZAG structure includes a large groove analogous to class I MHC peptide binding grooves. Instead of a peptide, the ZAG groove contains a nonpeptidic compound that may be implicated in lipid catabolism under normal or pathological conditions. IgC_MHC_I_alpha3; 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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
2FJH_L      134 CLLNNFYPREAKVQWKvdnalQSGNSQESVTEQD---SKDSTYSLSSTLTLSKADYEKhkvYACEVTHQGLSSPVT 206
Cdd:cd21010  23 CLAYDFYPRGISLHWT-----RAGKVQESESGGDvlpSGNGTYQSWVVVEVPPQDRAP---YSCHVEHSSLAQPLT 90

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
2FJH_L      130 ASVVCLLNNFYPREAKVQWKVDNALQSGNSqESVTEQDSKDSTYSLSSTLTLSKADYEKhkvYACEVTHQGLSSPVT 206
Cdd:cd21027  20 ATLRCWALSFYPAEITLTWQRDGEDQTQDT-ELVETRPAGDGTFQKWAAVVVPSGQEQR---YTCHVQHEGLPKPLT 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      119 PPSDEQlksgtASVVCLLNNFYPREAKVQWKVDNALQSGNSqESVTEQDSKDSTYSLSSTLTLSKADYEKhkvYACEVTH 198
Cdd:cd21023  14 PISDHE-----ATLRCWALGFYPAEITLTWQRDGEEQTQDT-ELVETRPAGDGTFQKWAAVVVPPGEEQR---YTCHVQH 84

                ....*..
2FJH_L      199 QGLSSPV 205
Cdd:cd21023  85 EGLPQPL 91

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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
2FJH_L      128 GTASVVCLLNNFYPREAKVQWKVdNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKhkvYACEVTHQGLSSPVT 206
Cdd:cd21020  18 GDVTLRCWALGFYPADITLTWQL-NGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQK---YTCHVEHEGLPEPLT 92

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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      113 PSVFIFPPsdeQLKSGTASVV--CLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL--SKADyek 188
Cdd:cd21002   4 PSVRVAPT---TPFNTREPVMlaCHVWGFYPADVTITWLKNGDPVAPHSSAPKTAQPNGDWTYQTQVTLAVtpSPGD--- 77

                        90
                ....*....|....*....
2FJH_L      189 hkVYACEVTHQGLSSPVTK 207
Cdd:cd21002  78 --TYTCSVQHASLPEPLLE 94

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) I-A; 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 alpha chain of histocompatibility antigen (HLA) I-A. 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 a 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.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
2FJH_L      112 APSVFIFPPSDEQLKSGTaSVVCLLNNFYPREAKVQWkVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEkhkV 191
Cdd:cd21006   2 APQATVFPKSPVLLGQPN-TLICFVDNIFPPVINITW-LRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDD---I 76

                        90
                ....*....|....*....
2FJH_L      192 YACEVTHQGLSSPVTKSFN 210
Cdd:cd21006  77 YDCKVEHWGLEEPVLKHWE 95