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Conserved domains on  [gi|6678219|ref|NP_033344|]
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tapasin isoform 2 precursor [Mus musculus]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 295-394 2.20e-15

Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of this group are components of immunoglobulin, neuroglia, cell surface glycoproteins, including T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, including butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond. Ig superfamily (IgSF) domains can be divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets. Typically, the V-set domains have A, B, E, and D strands in one sheet and A', G, F, C, C' and C" in the other. 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 by strands G, F, C, and C'. Moreover, a C1-set Ig domain contains a short C' strand (three residues) and lacks A' and C" strand. Unlike other Ig domain sets, C2-set structures do not have a D strand. Like the V-set Ig domains, members of the I-set have a discontinuous A strand, but lack a C" strand.


The actual alignment was detected with superfamily member cd05771:

Pssm-ID: 472250  Cd Length: 100  Bit Score: 71.76  E-value: 2.20e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  295 PRVSLTPAPVVWAapgEAPPELLCLASHFFPAEgLEVKWELRGGPGGSSRKVEGKTWLSTIRHHSDGSVSQSGHLQLPPV 374
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEPG 76

                        90       100
                ....*....|....*....|
gi 6678219  375 TAkQHGVHYVCRVYHSSLPA 394
Cdd:cd05771  77 TE-NRGATYTCRVTHVSLEE 95
 
Name Accession Description Interval E-value
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 295-394 2.20e-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: 71.76  E-value: 2.20e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  295 PRVSLTPAPVVWAapgEAPPELLCLASHFFPAEgLEVKWELRGGPGGSSRKVEGKTWLSTIRHHSDGSVSQSGHLQLPPV 374
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEPG 76

                        90       100
                ....*....|....*....|
gi 6678219  375 TAkQHGVHYVCRVYHSSLPA 394
Cdd:cd05771  77 TE-NRGATYTCRVTHVSLEE 95
C1-set pfam07654
Immunoglobulin C1-set domain;
313-392 9.08e-06

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 43.78  E-value: 9.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219    313 PPELLCLASHFFPAEgLEVKWELRGGPggssrkVEGKTWLSTIRHHSDGSVSQSGHLQLPPVTAKQHGVhYVCRVYHSSL 392
Cdd:pfam07654  14 PNTLTCLVTGFYPPD-ITVTWLKNGQE------VTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE-YTCRVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
316-393 3.64e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 3.64e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6678219     316 LLCLASHFFPAEgLEVKWELRGGPggssrkVEGKTWLSTIRHHSDGSVSQSGHLQLPPVTAKQHGVhYVCRVYHSSLP 393
Cdd:smart00407   4 LVCLVSGFYPPD-ITVTWLRNGQE------VTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDV-YTCQVTHEGLK 73
 
Name Accession Description Interval E-value
IgC1_Tapasin_R cd05771
Tapasin-R immunoglobulin-like domain; member of the C1-set of Ig superfamily (IgSF) domains; ...
 295-394 2.20e-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: 71.76  E-value: 2.20e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  295 PRVSLTPAPVVWAapgEAPPELLCLASHFFPAEgLEVKWELRGGPGGSSRKVEGKTWLSTIRHHSDGSVSQSGHLQLPPV 374
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEPG 76

                        90       100
                ....*....|....*....|
gi 6678219  375 TAkQHGVHYVCRVYHSSLPA 394
Cdd:cd05771  77 TE-NRGATYTCRVTHVSLEE 95
IgC1 cd00098
Immunoglobulin Constant-1 (C1)-set domain; The members here are composed of C1-set domains, ...
 296-395 1.21e-11

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: 60.94  E-value: 1.21e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  296 RVSLTPAPVvwAAPGEAPPELLCLASHFFPAEgLEVKWELRGGPGGSSrkvegkTWLSTIRHHSDGSVSQSGHLQLPPVT 375
Cdd:cd00098   1 TVTLLPPSP--EEKGGGKVTLVCLVSGFYPKD-ITVTWLKNGVPLTSG------VSTSSPVEPNDGTYSVTSSLTVPPSD 71

                        90       100
                ....*....|....*....|
gi 6678219  376 AKqHGVHYVCRVYHSSLPAS 395
Cdd:cd00098  72 WD-EGATYTCVVTHESLKSP 90
C1-set pfam07654
Immunoglobulin C1-set domain;
313-392 9.08e-06

Immunoglobulin C1-set domain;


Pssm-ID: 462221  Cd Length: 85  Bit Score: 43.78  E-value: 9.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219    313 PPELLCLASHFFPAEgLEVKWELRGGPggssrkVEGKTWLSTIRHHSDGSVSQSGHLQLPPVTAKQHGVhYVCRVYHSSL 392
Cdd:pfam07654  14 PNTLTCLVTGFYPPD-ITVTWLKNGQE------VTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDE-YTCRVEHEGL 85
IGc1 smart00407
Immunoglobulin C-Type;
316-393 3.64e-05

Immunoglobulin C-Type;


Pssm-ID: 214651  Cd Length: 75  Bit Score: 41.92  E-value: 3.64e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 6678219     316 LLCLASHFFPAEgLEVKWELRGGPggssrkVEGKTWLSTIRHHSDGSVSQSGHLQLPPVTAKQHGVhYVCRVYHSSLP 393
Cdd:smart00407   4 LVCLVSGFYPPD-ITVTWLRNGQE------VTEGVSTTDPLKNSDGTYFLSSYLTVPASTWESGDV-YTCQVTHEGLK 73
IgC1_CD1 cd21029
Immunoglobulin domain of Cluster of Differentiation (CD) 1; member of the C1-set of Ig ...
 293-393 3.65e-05

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: 42.31  E-value: 3.65e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  293 KAPRVSLTPAPvvwaAPGEAPPELLCLASHFFPAEgLEVKWeLRGGpggssRKVEGKTWLSTIRHHSDGSVSQSGHLQLP 372
Cdd:cd21029   1 VKPRVRLSSRP----SPGDGHLQLSCHVTGFYPRP-IEVTW-LRDG-----QEQMDGTQSGGILPNHDGTYQLRKTLDIA 69

                        90       100
                ....*....|....*....|.
gi 6678219  373 PvtAKQHGvhYVCRVYHSSLP 393
Cdd:cd21029  70 P--GEGAG--YSCRVDHSSLK 86
IgC1_MHC_II_beta cd05766
Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain; member of ...
 295-393 8.87e-03

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: 35.77  E-value: 8.87e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6678219  295 PRVSLTPAPVVwaaPGEAPPELLCLASHFFPAEgLEVKWELRGgpggsSRKVEGKTWLSTIRHhSDGSVSQSGHLQLPPv 374
Cdd:cd05766   4 PSVKVSPTKTG---PLEHPNLLVCSVTGFYPAE-IEVKWFRNG-----QEETAGVVSTELIPN-GDWTFQILVMLETTP- 72

                        90
                ....*....|....*....
gi 6678219  375 takQHGVHYVCRVYHSSLP 393
Cdd:cd05766  73 ---RRGDVYTCQVEHSSLQ 88
 
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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