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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        2 IVITQSPSLLSASVGDRVTLTCKGSQNI-DNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTDYTLTISSLHS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSIsSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
5HBV_C       81 EDLATYYCYQYING-YTFGTGTKLEL 105
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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        2 IVITQSPSLLSASVGDRVTLTCKGSQNI-DNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTDYTLTISSLHS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSIsSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
5HBV_C       81 EDLATYYCYQYING-YTFGTGTKLEL 105
Cdd:cd04980  81 EDAAVYYCQQGYTFpYTFGGGTKLEI 106

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        114 VSIFPPSTEQLaTGGASVVCLMNNFYPRDISVKWKIDGTERRDGVlDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTC 193
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78

                  ....*..
5HBV_C        194 EVVHKTS 200
Cdd:pfam07654  79 RVEHEGL 85

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
5HBV_C          19 VTLTCK--GSQNIDNYLAWYQQKLGEAPKLLIYKTNS----LQTGIPSRFSGSG--SGTDYTLTISSLHSEDLATYYC 88
Cdd:smart00406   2 VTLSCKfsGSTFSSYYVSWVRQPPGKGLEWLGYIGSNgssyYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYC 79

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        2 IVITQSPSLLSASVGDRVTLTCKGSQNI-DNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTDYTLTISSLHS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSIsSNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
5HBV_C       81 EDLATYYCYQYING-YTFGTGTKLEL 105
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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        3 VITQSPSLlSASVGDRVTLTCKGSQNI--DNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTDYTLTISSLHS 80
Cdd:cd04984   1 VLTQPSSL-SVSPGETVTITCTGSSGNisGNYVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQT 79

                        90       100
                ....*....|....*....|....
5HBV_C       81 EDLATYYCYQ-YINGYTFGTGTKL 103
Cdd:cd04984  80 EDEADYYCQVwDSNSYVFGGGTKL 103

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        4 ITQSPSLLSASVGDRVTLTCKGSQ-NIDNYLAWYQQKLGEAPKLLIYKTNSLQT---GIPSRFSGSGSG-TDYTLTISSL 78
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSsFSSTYIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLTISNL 80

                        90       100       110
                ....*....|....*....|....*....|
5HBV_C       79 HSEDLATYYCYQYING----YTFGTGTKLE 104
Cdd:cd00099  81 QPEDSGTYYCAVSESGgtdkLTFGSGTRLT 110

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      113 TVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVlDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYT 192
Cdd:cd00098   1 TVTLLPPSPEEKGGGKVTLVCLVSGFYPKDITVTWLKNGVPLTSGV-STSSPVEPNDGTYSVTSSLTVPPSDWDEGATYT 79

                        90
                ....*....|....*.
5HBV_C      193 CEVVHKTSSSPVVKSF 208
Cdd:cd00098  80 CVVTHESLKSPLSKTW 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      112 PTVSIFPPSTEQLATGG-ASVVCLMNNFYPRDISVKWKIDGTER-RDGVLDSVTDQDSkDSTYSMSSTLSLTKADYESHN 189
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPLpSADYKTTAPVPES-DGSFFVYSKLNVSTADWNSGD 79

                        90       100
                ....*....|....*....|...
5HBV_C      190 LYTCEVVHKTSSSPVV-KSFNRN 211
Cdd:cd05768  80 VFSCVVGHEALPLQFTqKSIDKS 102

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        4 ITQSPSLLSASVGDRVTLTCKGSQNIDNYLAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGS--GSGTDYTLTISSLHSE 81
Cdd:cd04983   1 VTQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDSGNKKKGRFSATldKSRKSSSLHISAAQLS 80

                        90       100
                ....*....|....*....|....*.
5HBV_C       82 DLATYYC----YQYINGYTFGTGTKL 103
Cdd:cd04983  81 DSAVYFCalseSGGTGKLTFGKGTRL 106

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
5HBV_C          19 VTLTCK--GSQNIDNYLAWYQQKLGEAPKLLIYKTNS----LQTGIPSRFSGSG--SGTDYTLTISSLHSEDLATYYC 88
Cdd:smart00406   2 VTLSCKfsGSTFSSYYVSWVRQPPGKGLEWLGYIGSNgssyYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYC 79

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C          6 QSPSLLSASVGDRVTLTC--KGSQNIDN-YLAWYQQKLGEAPKLLI-YKTNSLQTGIPS-RFSGSG--SGTDYTLTISSL 78
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCtySSSMSEAStSVYWYRQPPGKGPTFLIaYYSNGSEEGVKKgRFSGRGdpSNGDGSLTIQNL 80

                          90       100
                  ....*....|....*....|....*.
5HBV_C         79 HSEDLATYYCYQYINGY-TFGTGTKL 103
Cdd:pfam07686  81 TLSDSGTYTCAVIPSGEgVFGKGTRL 106

CH2 domain (second constant Ig domain of the heavy chain) in immunoglobulin E (IgE); member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the second constant domain of the heavy chain of immunoglobulin E (IgE). The basic structure of immunoglobulin (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). The different classes of antibodies vary in their heavy chains; the IgE class has the epsilon type. This domain (Cepsilon2) of IgE is in place of the flexible hinge region found in IgG.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      112 PTVSIFPPSTEQLATGGA-SVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSkDSTYSMSSTLSLTKADYESHNL 190
Cdd:cd05847   1 PTVQILHSSCASTLTSETiQLLCLISGYTPSTIEVEWLVDGQVATLSAASTAPQKEE-GGTFSTTSKLNVTQEDWKSGKT 79

                ....*..
5HBV_C      191 YTCEVVH 197
Cdd:cd05847  80 YTCKVTH 86

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      125 ATGGASV--VCLMNNFYPRDISVKWKIDGTERRDgvLDSVTDQDSKDSTYSMSST--LSLTKADYESHnlYTCEVVHKTS 200
Cdd:cd05772  14 ATPGQTVsfTCKSHGFSPRDITLKWFKNGNELSA--LQTTVFPEGDSVSYSVSSTvqVVLTKDDVHSQ--LTCEVAHVTL 89

                ....*....
5HBV_C      201 SSPVVKSFN 209
Cdd:cd05772  90 QAPLRGTAN 98

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        4 ITQSPSLLSASVGDRVTLTCKGSQNIDNY-LAWYQQKLGEAPKLLIYKTNSLQTGIPSRFSGSGSGTD--YTLTISSLHS 80
Cdd:cd07706   2 VTQAQPDVSVQVGEEVTLNCRYETSWTNYyLFWYKQLPSGEMTFLIRQDSSEQNAKSGRYSVNFQKAQksISLTISALQL 81

                        90       100
                ....*....|....*....|....*..
5HBV_C       81 EDLATYYCYQYINGYT----FGTGTKL 103
Cdd:cd07706  82 EDSAKYFCALSLPYDTdkliFGKGTRL 108

Class II major histocompatibility complex (MHC) beta chain immunoglobulin domain of histocompatibility antigen (HLA) DQ and I-A; 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 human histocompatibility antigen (HLA) DQ and mouse 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 have the same basic features insofar as peptide loading and presentation, they differ in that each interacts with distinctly different sets of peptides, and in the incidence of deletion of their genes. A structural understanding of the similarities and differences between I-A and I-E may help with understanding their roles 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. Human HLA-DR, -DQ, and -DP 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. HLA-DQ is involved in the autoimmune diseases celiac disease and diabetes mellitus type. DQ is one of several antigens involved in rejection of organ transplants. DQ2 is encoded by the HLA-DQB1*02 allele group. DQ6 is encoded by the HLA-DQB1*06 allele group. DQ2 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. These isoforms, nicknamed DQ2.2 and DQ2.5, are also encoded by the DQA1*0201 and DQA1*0501 genes, respectively. DQ6 beta-chains combine with alpha-chains, encoded by genetically linked HLA-DQA1 alleles, to form the cis-haplotype isoforms. For DQ6, however, cis-isoform pairing only occurs with DQ1 alpha-chains. There are many haplotypes of DQ6. Susceptibility to Leptospirosis infection was found associated with undifferentiated DQ6. DQ8 is determined by the antibody recognition of beta8 and this generally detects the gene product of DQB1*0302. DQ8 is commonly linked to autoimmune disease in the human population. DQ8 is the second most predominant isoform linked to celiac disease and the DQ most linked to Type 1 diabetes. DQ8 increases the risk for rheumatoid arthritis and is linked to the primary risk locus for RA, HLA-DR4. DR4 also plays an important role in Type 1 diabetes. 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 response. They are expressed constitutively on the cell surface of professional antigen-presenting cells (APCs), including B-lymphocytes, monocytes, and macrophages in both humans and mice, and induced in nonprofessional APCs, such as keratinocyctes; they are expressed on the surface of activated human T cells and on T cells from other species. 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, and 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      110 AAPTVSIFPPSTEQLaTGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSkDSTYSMSSTLSLTKadyESHN 189
Cdd:cd21001   2 VEPTVTISPSRTEAL-NHHNLLVCSVTDFYPGQIKVRWFRNDQEETAGVVSTPLIRNG-DWTFQILVMLEMTP---QRGD 76

                        90
                ....*....|....*
5HBV_C      190 LYTCEVVHKTSSSPV 204
Cdd:cd21001  77 VYTCHVEHPSLQSPI 91

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C        7 SPSLLSASVGDRVTLTCKGSQNIDNYLAWYQQKLGEAPKL--LIYKTNSLQTGIP-----SRFSGSGSGTDYTLTISSLH 79
Cdd:cd05720   4 SPRKRDAQLGQKVELVCEVLNSVPQGCSWLFQPRGSAPQPtfLLYLSSSNKTKWAegldsKRFSGSRSGSSYVLTLKDFR 83

                        90
                ....*....|....
5HBV_C       80 SEDLATYYCYQYIN 93
Cdd:cd05720  84 KEDEGYYFCSVISN 97

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      111 APTVSIFppSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVlDSVTDQDSKDSTYSMSSTLSLTKADYEShnl 190
Cdd:cd21029   2 KPRVRLS--SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGT-QSGGILPNHDGTYQLRKTLDIAPGEGAG--- 75

                        90
                ....*....|....*
5HBV_C      191 YTCEVVHKTSSSPVV 205
Cdd:cd21029  76 YSCRVDHSSLKQDLI 90

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      112 PTVSIFPPSTEQL-ATGGASVVCLMNNFYPRD-ISVKW-KIDGTErrdgVLDSVTDQDSK-DSTYSMSSTLSLTKADYES 187
Cdd:cd07696   1 VSVFLIPPSPKDLfLTKSAKVTCLVVDLTSIEeVNVTWsREDGNE----VLASTTNPEKHyNATLSVVSTLTVCADDWDN 76

                        90       100
                ....*....|....*....|
5HBV_C      188 HNLYTCEVVHKTSSSPVVKS 207
Cdd:cd07696  77 GKTFKCKVTHPDLPSPIVKS 96

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      111 APTVSIFPPSTEQLatGGASV-VCLMNNFYPRDISVKWKIDGTERRDGVLDSVTdQDSKDSTYSMSSTLSLTKadyESHN 189
Cdd:cd05767   2 PPEVTVFPKSPVEL--GEPNTlICFVDNFFPPVINVTWLRNGQPVTDGVSETVF-LPREDHSFRKFSYLPFTP---SEGD 75

                        90
                ....*....|....*..
5HBV_C      190 LYTCEVVHKTSSSPVVK 206
Cdd:cd05767  76 IYDCRVEHWGLEEPLLK 92

CH1 domain (first constant Ig domain of the heavy chain) in immunoglobulin heavy mu 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 mu 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      111 APTVsiFP-PSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLD--SVTdqdsKDSTYSMSSTLSLTKADYES 187
Cdd:cd21819   1 APTL--FPlVSCGSSTSDPVTVGCLATDFLPDSITFSWTDDNNSLTTGVKTypSVL----TGGTYTASSQLQVPESEWKS 74

                        90
                ....*....|
5HBV_C      188 HNLYTCEVVH 197
Cdd:cd21819  75 KENFYCKVEH 84

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      111 APTVSIFPPSTEQLATGGaSVVCLMNNFYPRDISVKWKIDGTERRDGVLDSvTDQDSKDSTYSMSSTLSLTKADyesHNL 190
Cdd:cd21006   2 APQATVFPKSPVLLGQPN-TLICFVDNIFPPVINITWLRNSKSVTDGVYET-SFLVNRDHSFHKLSYLTFIPSD---DDI 76

                        90
                ....*....|....*....
5HBV_C      191 YTCEVVHKTSSSPVVKSFN 209
Cdd:cd21006  77 YDCKVEHWGLEEPVLKHWE 95

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
5HBV_C       16 GDRVTLTCKGSQNIDNYLAW---YQQK-LGEAPKLLIYKTNSLQTGIPSRFSGSGSGTdYTLTISSLHSEDLATYYC 88
Cdd:cd07690   9 GDTAELPCTASQKKSIQFHWknsNQIKiLGNQGSFLTKGPSKLNDRADSRRNLWDQGS-FPLIIKNLKIEDSDTYIC 84

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      112 PTVSIFPpSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKadyESHNLY 191
Cdd:cd21002   4 PSVRVAP-TTPFNTREPVMLACHVWGFYPADVTITWLKNGDPVAPHSSAPKTAQPNGDWTYQTQVTLAVTP---SPGDTY 79

                        90
                ....*....|....*
5HBV_C      192 TCEVVHKTSSSPVVK 206
Cdd:cd21002  80 TCSVQHASLPEPLLE 94

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
5HBV_C      127 GGASVVCLMNNFYPRDISVKWKIDGTERRDGvLDSVTDQDSKDSTYSMSSTLSLTKADYEShnlYTCEVVHKTSSSPVV 205
Cdd:cd21016  18 GDVTLRCWALGFYPADITLTWQKDGEELTQD-MEFVETRPAGDGTFQKWAAVVVPLGKEQS---YTCHVYHEGLPEPLT 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      127 GGASVVCLMNNFYPRDISVKWKIDGTERrdgvldsvtDQDSK--------DSTYSMSSTLsltKADYESHNLYTCEVVHK 198
Cdd:cd07698  15 GESTLRCWALGFYPAEITLTWQRDGEDQ---------TQDMElvetrpngDGTFQKWAAV---VVPSGEEQRYTCHVQHE 82

                ....*..
5HBV_C      199 TSSSPVV 205
Cdd:cd07698  83 GLPEPLT 89

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
5HBV_C      112 PTVsiFPPSTEQLATGGASVV-CLMNNFYPRDISVKWKIDGterRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNL 190
Cdd:cd21818   2 PTV--FPLSLCPSLSSDPVVIgCLVQGFFPEPVNVTWNYSG---KGGTARNFPAMLASGGRYTQSSQLTLPADQCPEGEA 76

                        90
                ....*....|.
5HBV_C      191 YTCEVVHKTSS 201
Cdd:cd21818  77 YKCSVQHYSPS 87

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
5HBV_C      133 CLMNNFYPRDISVKWKIDGTERRDGvLDSVTDQDSKDSTYS--MSSTLSLTKADYeshnlYTCEVVHKTSSSPV 204
Cdd:cd21019  23 CWALGFYPADITLTWQLNGEELIQD-MELVETRPAGDGTFQkwASVVVPLGKEQY-----YTCHVYHQGLPEPL 90