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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   3 ELTQPRSVSGSPGQSVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLIIHDVIIRPSGVPDRFSGSKSGNTASLTISGLQA 82
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGN-YVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                         90       100
                 ....*....|....*....|....*.
gi 237824083  83 EDEAHYYCWSFAGSYYVFGTGTDVTV 108
Cdd:cd04984   80 EDEADYYCQVWDSNSYVFGGGTKLTV 105

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   3 ELTQPRSVSGSPGQSVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLIIHDVIIRPSGVPDRFSGSKSGNTASLTISGLQA 82
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGN-YVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                         90       100
                 ....*....|....*....|....*.
gi 237824083  83 EDEAHYYCWSFAGSYYVFGTGTDVTV 108
Cdd:cd04984   80 EDEADYYCQVWDSNSYVFGGGTKLTV 105

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083  118 VTLFPPSSEELQaNKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQ 197
Cdd:pfam07654   1 VYVFPPSPEELG-KPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 237824083  198 VTHEGN 203
Cdd:pfam07654  80 VEHEGL 85

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083    5 TQPRSVSGSPGQSVTISCTGTSRDVGGYNYVSWYQQHPGKAPKLIIH--DVIIRPSGVPDRFSGSK--SGNTASLTISGL 80
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSEASTSVYWYRQPPGKGPTFLIAyySNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 237824083   81 QAEDEAHYYCWSFAGSYYVFGTGTDVTVL 109
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTVL 109

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   3 ELTQPRSVSGSPGQSVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLIIHDVIIRPSGVPDRFSGSKSGNTASLTISGLQA 82
Cdd:cd04984    1 VLTQPSSLSVSPGETVTITCTGSSGNISGN-YVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                         90       100
                 ....*....|....*....|....*.
gi 237824083  83 EDEAHYYCWSFAGSYYVFGTGTDVTV 108
Cdd:cd04984   80 EDEADYYCQVWDSNSYVFGGGTKLTV 105

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083  118 VTLFPPSSEELQaNKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQ 197
Cdd:pfam07654   1 VYVFPPSPEELG-KPNTLTCLVTGFYPPDITVTWLKNGQEVTEGVKTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTCR 79

                  ....*.
gi 237824083  198 VTHEGN 203
Cdd:pfam07654  80 VEHEGL 85

Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin variable domain (IgV). The IgV family contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology, and are components of immunoglobulin (Ig) and T cell receptors. 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. Within the variable domain, there are regions of even more variability called the hypervariable or complementarity-determining regions (CDRs) which are responsible for antigen binding. A predominant feature of most Ig domains is the disulfide bridge connecting 2 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" strands in the other.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   4 LTQ-PRSVSGSPGQSVTISCTGTSRDvgGYNYVSWYQQHPGKAPKLIIH---DVIIRPSGVPDRFSGSKSG-NTASLTIS 78
Cdd:cd00099    1 VTQsPRSLSVQEGESVTLSCEVSSSF--SSTYIYWYRQKPGQGPEFLIYlssSKGKTKGGVPGRFSGSRDGtSSFSLTIS 78

                         90       100       110
                 ....*....|....*....|....*....|...
gi 237824083  79 GLQAEDEAHYYC---WSFAGSYYVFGTGTDVTV 108
Cdd:cd00099   79 NLQPEDSGTYYCavsESGGTDKLTFGSGTRLTV 111

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 117 TVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRSYSC 196
Cdd:cd00098    1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGVSTSSPVEPNDGTYSVTSSLTVPPSDWDEGATYTC 80

                         90
                 ....*....|....*
gi 237824083 197 QVTHEGN--TVEKTV 209
Cdd:cd00098   81 VVTHESLksPLSKTW 95

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEEL-QANKATLVCLISDFYPGAVTVAWKADGSPV-KAGVETTKPSKQSNNKYAASSYLSLTPEQWKSHRS 193
Cdd:cd05768    1 PSVYLLPPPEEELsLNETVTLTCLVKGFYPEDIFVSWLQNGEPLpSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                         90
                 ....*....|....*....
gi 237824083 194 YSCQVTHEG---NTVEKTV 209
Cdd:cd05768   81 FSCVVGHEAlplQFTQKSI 99

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

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083    5 TQPRSVSGSPGQSVTISCTGTSRDVGGYNYVSWYQQHPGKAPKLIIH--DVIIRPSGVPDRFSGSK--SGNTASLTISGL 80
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYSSSMSEASTSVYWYRQPPGKGPTFLIAyySNGSEEGVKKGRFSGRGdpSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*....
gi 237824083   81 QAEDEAHYYCWSFAGSYYVFGTGTDVTVL 109
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEGVFGKGTRLTVL 109

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083    17 SVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLII----HDVIIRPSGVPDRFSGSK--SGNTASLTISGLQAEDEAHYYC 90
Cdd:smart00406   1 SVTLSCKFSGSTFSSY-YVSWVRQPPGKGLEWLGyigsNGSSYYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYC 79

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins; The members here are composed of the immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). 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 represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens directly without antigen processing and recognize MHC independently of the bound peptide. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   5 TQ-PRSVSGSPGQSVTISCTGTSRdvgGYNYVSWYQQHPGKAPKLIIHDVIIRPSGVPDRFSGS--KSGNTASLTISGLQ 81
Cdd:cd04983    2 TQsPQSLSVQEGENVTLNCNYSTS---TFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQ 78

                         90       100       110
                 ....*....|....*....|....*....|
gi 237824083  82 AEDEAHYYC-WSFAGSYY--VFGTGTDVTV 108
Cdd:cd04983   79 LSDSAVYFCaLSESGGTGklTFGKGTRLTV 108

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEEL-QANkaTLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEqwkSHRSY 194
Cdd:cd05767    3 PEVTVFPKSPVELgEPN--TLICFVDNFFPPVINVTWLRNGQPVTDGVSETVFLPREDHSFRKFSYLPFTPS---EGDIY 77

                 ....*...
gi 237824083 195 SCQVTHEG 202
Cdd:cd05767   78 DCRVEHWG 85

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 115 NPTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSK-QSNNKYAASSYLSLTPEQWKSHRS 193
Cdd:cd04985    1 APTVFPLQSATKSQSNGPVALGCLISDYFPESITVSWQKNTNSITSGFTRTFPVVlRSGGDYSCSSQLTVPLQEWNSGEV 80

                         90
                 ....*....|
gi 237824083 194 YSCQVTHEGN 203
Cdd:cd04985   81 YKCQVQHSAS 90

Immunoglobulin (Ig) heavy chain (H), variable (V) domain; The members here are composed of the immunoglobulin (Ig) heavy chain (H), 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. 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 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 can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   3 ELTQPRSVSGSPGQSVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLIihdVIIRPSG--------VPDRFSGS--KSGNT 72
Cdd:cd04981    1 QLQESGPGLVKPGQSLKLSCKASGFTFTSY-GMGWVRQAPGKGLEWI---GLIYPGGgdtyyadsFKGRFTITrdTSKST 76

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 237824083  73 ASLTISGLQAEDEAHYYC-----WSFAGSYYVFGTGTDVTV 108
Cdd:cd04981   77 AYLQLNSLTSEDTAVYYCarglgGYGYSYFDYWGQGTTVTV 117

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 113 KANPTVTLFPPSSEELQANKaTLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEqwkSHR 192
Cdd:cd20998    4 RVEPTVTVYPTKTQPLEHHN-LLVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNGDWTFQTLVMLETVPQ---SGE 79

                         90
                 ....*....|....*..
gi 237824083 193 SYSCQVTHEGNTVEKTV 209
Cdd:cd20998   80 VYTCQVEHPSLTDPVTV 96

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 113 KANPTVTLFPPSSEELQANKaTLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPeqwKSHR 192
Cdd:cd21000    1 RVEPKVTVYPAKTQPLQHHN-LLVCSVNGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVP---RSGE 76

                         90
                 ....*....|....*..
gi 237824083 193 SYSCQVTHEGNTVEKTV 209
Cdd:cd21000   77 VYTCQVEHPSVTSPLTV 93

Class II major histocompatibility complex (MHC) alpha chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and related proteins; 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) DQ. MHC class II molecules are encoded by three different loci, HLA-DR, -DQ, and -DP, which are about 70% similar to each other. HLA-DQ (DQ) is a cell surface receptor protein found on antigen presenting cells. It is an alphabeta heterodimer of type MHC class II. The alpha and beta chains are encoded by two loci, HLA-DQA1 and HLA-DQB1, that are adjacent to each other on chromosome band 6p21.3. A person often produces two alpha-chain and two beta chain variants and thus 4 isoforms of DQ. Two autoimmune diseases in which HLA-DQ is involved are celiac disease and diabetes mellitus type 1. DQ is one of several antigens involved in rejection of organ transplants. DQ8 is a split antigen of the DQ3 broad antigen. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEEL-QANkaTLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEqwkSHRSY 194
Cdd:cd21008    3 PEVTVFPKSPVTLgQPN--TLICLVDNIFPPVINITWLSNGHSVTEGVSETSFLSKSDHSFLKISYLTFLPS---ADDIY 77

                 ....*...
gi 237824083 195 SCQVTHEG 202
Cdd:cd21008   78 DCKVEHWG 85

Gammadelta T-cell antigen receptor, variable (V) domain; The members here are composed of the immunoglobulin (Ig) variable (V) domain of the 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083   6 QPRSVSGSPGQSVTISCTGTSRDVGGYnYVSWYQQHPGKAPKLIIHDVIIRPSGVPDRFSGS--KSGNTASLTISGLQAE 83
Cdd:cd20988    4 EHQTVTVSVGKPVTLKCSMKGEAISNY-YINWYRKTQGNTMTFIYREGGIYGPGFKDNFRGDidSSNNLAVLKILEASER 82

                         90       100       110
                 ....*....|....*....|....*....|.
gi 237824083  84 DEAHYYCWS---FAGSYY---VFGTGTDVTV 108
Cdd:cd20988   83 DEGSYYCASdtpGGGREYdplIFGKGTYLTV 113

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLF-PPSSEelqaNKATLVCLISDFYPGAVTVAWKADGSPVKAGVET--TKPSkqSNNKYAASSYLSLTPEQWKshr 192
Cdd:cd07698    3 PKVHVThHPRSD----GESTLRCWALGFYPAEITLTWQRDGEDQTQDMELveTRPN--GDGTFQKWAAVVVPSGEEQ--- 73

                         90
                 ....*....|....*...
gi 237824083 193 SYSCQVTHEGNTVEKTVA 210
Cdd:cd07698   74 RYTCHVQHEGLPEPLTLR 91

Class II major histocompatibility complex (MHC) alpha 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 immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) DM. Human HLA-DM, also known as H2-M in mice, plays a critical role in antigen presentation to CD4 T cells by catalyzing the exchange of peptides bound to MHC class II molecules. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 237824083 134 TLVCLISDFYPGAVTVAWKADGSPVKaGVETTKPSKQSNNKYAASSYLSLTPEQWKshrSYSCQVTHE 201
Cdd:cd21009   20 TLVCFVSNLFPPMLTVNWQLHSVPVE-GFGPTFVSAVDGLSFQAFSYLNFTPEPSD---IFSCIVTHE 83

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 237824083 135 LVCLISDFYPGAVTVAWKADGSPVKAGvETTKPSKQSNN--KYAASSYLSLTPEQWKshrSYSCQVTH 200
Cdd:cd21002   22 LACHVWGFYPADVTITWLKNGDPVAPH-SSAPKTAQPNGdwTYQTQVTLAVTPSPGD---TYTCSVQH 85

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPpSSEELQANKATLVCLISDFYPGAVTVAW-----KADGSPV-KAGVETTKPSKQSNNKYAASSYLSLTPEQWK 189
Cdd:cd05771    1 PRVRLSP-KNLVKPDLPQTLSCHIAGYYPLDVDVEWlreepGGSESQVsRDGVSLSSHRQSVDGTYSISSYLTLEPGTEN 79

                         90
                 ....*....|..
gi 237824083 190 SHRSYSCQVTHE 201
Cdd:cd05771   80 RGATYTCRVTHV 91

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy epsilon and gamma 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 epsilon and gamma chains. It belongs to a family 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADGspVKAGVETTKPSKQSNNKYAASSYLSLtPEQWKSHRSYS 195
Cdd:cd21817    2 PSVFPLAPCCKSTNGSSVTLGCLVTGYFPEPVTVTWNSGS--LTSGVKTFPAVLQSSGLYTTSSQVTV-PSSSWGSQTFT 78

                 ....*
gi 237824083 196 CQVTH 200
Cdd:cd21817   79 CNVEH 83

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 112 PKANptVTLFPPSSEELqankaTLVCLISDFYPGAVTVAWKADGSPVKAGVE--TTKPSKQSNNKYAASSYLSLTPEQWk 189
Cdd:cd21820    6 PKAH--VTHHPRSEDEV-----TLRCWALGFYPADITLTWQLNGEELTQDMElvETRPAGDGTFQKWAAVVVPLGKEQY- 77

                         90
                 ....*....|...
gi 237824083 190 shrsYSCQVTHEG 202
Cdd:cd21820   78 ----YTCHVYHEG 86

Class II major histocompatibility complex (MHC) alpha 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 immunoglobulin (Ig) domain of major histocompatibility complex (MHC) class II alpha chain of histocompatibility antigen (HLA) I-E. 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEELqANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEqwkSHRSYS 195
Cdd:cd21005    3 PEVTVLSRSPVNL-GEPNILICFIDKFSPPVVNVTWLRNGRPVTEGVSETVFLPRDDHLFRKFHYLTFLPS---TDDFYD 78

                 ....*..
gi 237824083 196 CQVTHEG 202
Cdd:cd21005   79 CEVDHWG 85

CH2 domain (second 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 second immunoglobulin constant-1 set domain (IgC) of alpha 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. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPPSSEELQANK-ATLVCLISDFY-PGAVTVAWKADG--SPVkagveTTKPSKQSNNKYAASSYLSLTPEQWKSH 191
Cdd:cd04986    2 PRLSLQRPALEDLLLGSnASLTCTLSGLKdPEGATFTWEPSGgkEAI-----QGPPERDSCGCYSVSSVLPGCAEPWNSG 76

                         90
                 ....*....|....*...
gi 237824083 192 RSYSCQVTHEGNTVEKTV 209
Cdd:cd04986   77 DTFSCTVTHPESKGTLTA 94

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 237824083 131 NKATLVCLISDFYPGAVTVAWKADGSPVKAGVE--TTKPSKQSNNKYAASSYLSLTPEQWkshrsYSCQVTHEG 202
Cdd:cd21019   17 DKVTLRCWALGFYPADITLTWQLNGEELIQDMElvETRPAGDGTFQKWASVVVPLGKEQY-----YTCHVYHQG 85

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 237824083 116 PTVTLFPpSSEELQANKATLVCLISDFYPGAVTVAWKADGSPVKAGVETTKPSKQSNNKYAASSYLSLTPEqwkSHRSYS 195
Cdd:cd21006    3 PQATVFP-KSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPS---DDDIYD 78

                 ....*..
gi 237824083 196 CQVTHEG 202
Cdd:cd21006   79 CKVEHWG 85

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 237824083 134 TLVCLISDFYPGAVTVAWKADGSPVKAGVE--TTKPSKQSNNKYAASSYLSLTPEQwkshrSYSCQVTHEG 202
Cdd:cd21016   21 TLRCWALGFYPADITLTWQKDGEELTQDMEfvETRPAGDGTFQKWAAVVVPLGKEQ-----SYTCHVYHEG 86