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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   2 ILMTQSQKFLSTSVGDRVSVTCKASQNVG-TNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
gi 85544092  81 EDLAEYFCQQFNRYPLTFGSGTKLEL 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, kappa type, variable (V) domain. This group contains the standard Ig superfamily V-set AGFCC'C"/DEB domain topology. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   2 ILMTQSQKFLSTSVGDRVSVTCKASQNVG-TNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
gi 85544092  81 EDLAEYFCQQFNRYPLTFGSGTKLEL 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   115 VSIFPPSSEQLtSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTC 194
Cdd:pfam07654   1 VYVFPPSPEEL-GKPNTLTCLVTGFYPPDITVTWLKNGQEVTEGV-KTTPPSPNSDWTYQLSSYLTVTPSDWESGDEYTC 78

                  ....*..
gi 85544092   195 EATHKTS 201
Cdd:pfam07654  79 RVEHEGL 85

Immunoglobulin V-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092     19 VSVTCKASQ--NVGTNVAWYQQKPGQSPKPLMY----SASYRYSGVPDRFTGSG--SGTDFTLTISNVQSEDLAEYFCQQ 90
Cdd:smart00406   2 VTLSCKFSGstFSSYYVSWVRQPPGKGLEWLGYigsnGSSYYQESYKGRFTISKdtSKNDVSLTISNLRVEDTGTYYCAV 81

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   2 ILMTQSQKFLSTSVGDRVSVTCKASQNVG-TNVAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQS 80
Cdd:cd04980   1 IVMTQSPASLSVSPGERVTISCKASQSISsNYLAWYQQKPGQAPKLLIYYASTLHSGVPSRFSGSGSGTDFTLTISSVEP 80

                        90       100
                ....*....|....*....|....*.
gi 85544092  81 EDLAEYFCQQFNRYPLTFGSGTKLEL 106
Cdd:cd04980  81 EDAAVYYCQQGYTFPYTFGGGTKLEI 106

Immunoglobulin (Ig) lambda light chain variable (V) domain; The members here are composed of the immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. There are two types of light chains: kappa and lambda, each composed of a constant domain (CL) and a variable domain (VL). There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determines the type of immunoglobulin formed: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains. Members of this group contain standard Ig superfamily V-set AGFCC'C"/DEB domain topology.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092  11 LSTSVGDRVSVTCKASQ-NVGTN-VAWYQQKPGQSPKPLMYSASYRYSGVPDRFTGSGSGTDFTLTISNVQSEDLAEYFC 88
Cdd:cd04984   8 LSVSPGETVTITCTGSSgNISGNyVNWYQQKPGSAPRYLIYEDKHRPSGIPDRFSGSKSGNTASLTISGAQTEDEADYYC 87

                        90
                ....*....|....*.
gi 85544092  89 QQFNRYPLTFGSGTKL 104
Cdd:cd04984  88 QVWDSNSYVFGGGTKL 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   4 MTQSQKFLSTSVGDRVSVTCKASQNVGTN-VAWYQQKPGQSPKPLMYSASYRYS---GVPDRFTGSGSG-TDFTLTISNV 78
Cdd:cd00099   1 VTQSPRSLSVQEGESVTLSCEVSSSFSSTyIYWYRQKPGQGPEFLIYLSSSKGKtkgGVPGRFSGSRDGtSSFSLTISNL 80

                        90       100       110
                ....*....|....*....|....*....|
gi 85544092  79 QSEDLAEYFCQQF---NRYPLTFGSGTKLE 105
Cdd:cd00099  81 QPEDSGTYYCAVSesgGTDKLTFGSGTRLT 110

Immunoglobulin C-Type;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 85544092    130 ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSP 204
Cdd:smart00407   2 ATLVCLVSGFYPPDITVTWLRNGQEVTEGVSTTDPLKNS-DGTYFLSSYLTVPASTWESGDVYTCQVTHEGLKEP 75

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 113 PTVSIFPPSSEQLTSGG-ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Cdd:cd05768   1 PSVYLLPPPEEELSLNEtVTLTCLVKGFYPEDIFVSWLQNGEPLPSADYKTTAPVPESDGSFFVYSKLNVSTADWNSGDV 80

                        90       100
                ....*....|....*....|..
gi 85544092 192 YTCEATHKTSTSPIV-KSFNRN 212
Cdd:cd05768  81 FSCVVGHEALPLQFTqKSIDKS 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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   5 TQSQKFLSTSVGDRVSVTCKASQNVGTNVAWYQQKPGQSPKPLMYSASY-------RYSGVPDRFTGSgsgtdFTLTISN 77
Cdd:cd04983   2 TQSPQSLSVQEGENVTLNCNYSTSTFYYLFWYRQYPGQGPQFLIYISSDsgnkkkgRFSATLDKSRKS-----SSLHISA 76

                        90       100       110
                ....*....|....*....|....*....|
gi 85544092  78 VQSEDLAEYFC---QQFNRYPLTFGSGTKL 104
Cdd:cd04983  77 AQLSDSAVYFCalsESGGTGKLTFGKGTRL 106

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

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092     11 LSTSVGDRVSVTCKASQNVGTNVAWYQQKPgqspKPLMYsasyrysgvPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQQ 90
Cdd:smart00410   4 VTVKEGESVTLSCEASGSPPPEVTWYKQGG----KLLAE---------SGRFSVSRSGSTSTLTISNVTPEDSGTYTCAA 70

                           90
                   ....*....|....*
gi 85544092     91 FNRYPLTFGsGTKLE 105
Cdd:smart00410  71 TNSSGSASS-GTTLT 84

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 113 PTVSIFPPSSEQLTSGG-ASVVCFLNNFYPKDINVKWKIDGSERQ--NGVLNSWTDQDSKdSTYSMSSTLTLTKDEYERH 189
Cdd:cd16093   2 PTVSLHAPSREEFLGNRtATFVCLATGFSPKTISFKWLRNGKEVTssTGAVVEEPKEDGK-TLYSATSFLTITESEWKSQ 80

                        90
                ....*....|...
gi 85544092 190 NSYTCEATHKTST 202
Cdd:cd16093  81 TEFTCEFKHKGEI 93

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 113 PTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKDEYERHNS 191
Cdd:cd05847   1 PTVQILHSSCaSTLTSETIQLLCLISGYTPSTIEVEWLVDGQVATLSAASTAPQKEE-GGTFSTTSKLNVTQEDWKSGKT 79

                        90
                ....*....|.
gi 85544092 192 YTCEATHKTST 202
Cdd:cd05847  80 YTCKVTHQGTT 90

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 85544092 113 PTVSIFPpSSEQLTSGGASVVCFLNNFYPKDINVKWKID---GSERQNGVLNSW--TDQDSKDSTYSMSSTLTLTKDEYE 187
Cdd:cd05771   1 PRVRLSP-KNLVKPDLPQTLSCHIAGYYPLDVDVEWLREepgGSESQVSRDGVSlsSHRQSVDGTYSISSYLTLEPGTEN 79

                        90       100
                ....*....|....*....|.
gi 85544092 188 RHNSYTCEATHKTSTSPIVKS 208
Cdd:cd05771  80 RGATYTCRVTHVSLEEPLSVS 100

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 112 APTVSIFppSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVlNSWTDQDSKDSTYSMSSTLTLTKDEYErhnS 191
Cdd:cd21029   2 KPRVRLS--SRPSPGDGHLQLSCHVTGFYPRPIEVTWLRDGQEQMDGT-QSGGILPNHDGTYQLRKTLDIAPGEGA---G 75

                        90
                ....*....|....*
gi 85544092 192 YTCEATHKTSTSPIV 206
Cdd:cd21029  76 YSCRVDHSSLKQDLI 90

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 85544092 113 PTVSIFPPSSEQLTSGGAsVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYsmsSTLTLTKDEYERHNSY 192
Cdd:cd20998   7 PTVTVYPTKTQPLEHHNL-LVCSVSDFYPGNIEVRWFRNGKEEKTGIVSTGLVRNG-DWTF---QTLVMLETVPQSGEVY 81

                        90
                ....*....|...
gi 85544092 193 TCEATHKTSTSPI 205
Cdd:cd20998  82 TCQVEHPSLTDPV 94

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 113 PTVSIFPPSSEQL-TSGGASVVCFLNNFYPKD-INVKWKidgseRQNG--VLNS-WTDQDSKDSTYSMSSTLTLTKDEYE 187
Cdd:cd07696   1 VSVFLIPPSPKDLfLTKSAKVTCLVVDLTSIEeVNVTWS-----REDGneVLAStTNPEKHYNATLSVVSTLTVCADDWD 75

                        90       100
                ....*....|....*....|.
gi 85544092 188 RHNSYTCEATHKTSTSPIVKS 208
Cdd:cd07696  76 NGKTFKCKVTHPDLPSPIVKS 96

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 118 FPPS---SEQLTSGG--ASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDqdSKDSTYSMSSTLTLTKDEYERHNSY 192
Cdd:cd16085   1 VPPTlevTQQPTMVWnqVNVTCQVEKFYPQRLQLTWLENGNVSRTETPSTLTV--NKDGTYNWTSWLLVNVSAHREDVVL 78

                ....*.
gi 85544092 193 TCEATH 198
Cdd:cd16085  79 TCQVEH 84

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 112 APTVSIFPPSS-EQLTSGGASVVCFLNNFYPKDINVKWKIDGSER--QNGVLNSWTDQDskdsTYSMSSTLTLTKDEYEr 188
Cdd:cd07697   1 SPKPTIFLPSIaETEKQKAGTYLCLLENFFPDVIKIHWREKKSDTilESQEGNTEKTKD----TYMKFSWLTVPKKSLG- 75

                        90
                ....*....|.
gi 85544092 189 hNSYTCEATHK 199
Cdd:cd07697  76 -KEHRCIYKHE 85

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092  15 VGDRVSVTCKASQNVGTNVAWYQQKPGQSPKP--LMYSASYRYSGVPD-----RFTGSGSGTDFTLTISNVQSEDLAEYF 87
Cdd:cd05720  12 LGQKVELVCEVLNSVPQGCSWLFQPRGSAPQPtfLLYLSSSNKTKWAEgldskRFSGSRSGSSYVLTLKDFRKEDEGYYF 91

                .
gi 85544092  88 C 88
Cdd:cd05720  92 C 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 113 PTVsiFPPSSEQ-LTSGGASVVCFLNNFYPKDINVKWKIDGSErqnGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNS 191
Cdd:cd21818   2 PTV--FPLSLCPsLSSDPVVIGCLVQGFFPEPVNVTWNYSGKG---GTARNFPAMLASGGRYTQSSQLTLPADQCPEGEA 76

                        90
                ....*....|.
gi 85544092 192 YTCEATHKTST 202
Cdd:cd21818  77 YKCSVQHYSPS 87

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

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 85544092 133 VCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSkDSTYSMSSTLTLTKdeyERHNSYTCEATHKTSTSPI 205
Cdd:cd21003  23 VCHVTDFYPGNIQVRWFLNGQEETAGVVSTNLIHNG-DWTFQILVMLEMTP---QQGDVYTCQVEHPSLDSPV 91

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 85544092  16 GDRVSVTCKASQNVGTN--VAWYQQKPGQSPKPLMY-----SASYRYSGVPDRFTGS--GSGTDFTLTISNVQSEDLAEY 86
Cdd:cd04981  13 GQSLKLSCKASGFTFTSygMGWVRQAPGKGLEWIGLiypggGDTYYADSFKGRFTITrdTSKSTAYLQLNSLTSEDTAVY 92

                ..
gi 85544092  87 FC 88
Cdd:cd04981  93 YC 94

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   6 QSQKFLSTSVGDRVSVTCKA-SQNVGTNVAWYQQKPGQSP-KPLMYSASYRYSGV--------PDRFT--GSGSGTDFTL 73
Cdd:cd07700   3 QTPGSLLVQTNQTVKMSCEAkTSPKNTRIYWLRQRQAPSKdSHFEFLASWDPSKGivygegvdQEKLIilSDSDSSRYIL 82

                        90       100       110
                ....*....|....*....|....*....|.
gi 85544092  74 TISNVQSEDLAEYFCQQFNRYPLTFGSGTKL 104
Cdd:cd07700  83 SLMSVKPEDSGTYFCMTVGSPELIFGTGTKL 113

Second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor_like-1(FGFRL1); member of the I-set of IgSF domains; The members here are composed of the second immunoglobulin (Ig)-like domain of fibroblast growth factor (FGF) receptor like-1(FGFRL1). FGFRL1 is comprised of a signal peptide, three extracellular Ig-like modules, a transmembrane segment, and a short intracellular domain. FGFRL1 is expressed preferentially in skeletal tissues. Similar to FGF receptors, the expressed protein interacts specifically with heparin and with FGF2. FGFRL1 does not have a protein tyrosine kinase domain at its C-terminus; neither does its cytoplasmic domain appear to interact with a signaling partner. It has been suggested that FGFRL1 may not have any direct signaling function, but instead acts as a decoy receptor trapping FGFs and preventing them from binding other receptors.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   5 TQSQKF----LSTSVGDRVSVTCKASQNVGTNVAWYQ-QKPGQSPKPlmysasyrysgvpdrftGSGSGTDFTLTISNVQ 79
Cdd:cd05856   4 TQPAKMrrrvIARPVGSSVRLKCVASGNPRPDITWLKdNKPLTPPEI-----------------GENKKKKWTLSLKNLK 66

                        90
                ....*....|....
gi 85544092  80 SEDLAEYFCQQFNR 93
Cdd:cd05856  67 PEDSGKYTCHVSNR 80

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092 107 KRADAAPTVSIFPPSSEQltsgGASVVCFLNNFYPKDINVKWKIDGsERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEY 186
Cdd:cd21026   1 QRADPPKTHVTHHPISDH----EATLRCWALGFYPAEITLTWQRDG-EDQTQDTELVETRPAGDRTFQKWAAVVVPSGEE 75

                        90
                ....*....|....*....
gi 85544092 187 ERhnsYTCEATHKTSTSPI 205
Cdd:cd21026  76 QR---YTCHVQHEGLPKPL 91

Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains; The members here are composed of the immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (also known as cluster of differentiation (CD) 140a), and beta (also known as CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,PDGF-B, and PDGF-C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 85544092 144 INVKWKIDGSERQNGVLNSwtdQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFN 210
Cdd:cd05861  32 VDLEWTYPGKESGRGIEPV---EEFKVPPYHLVYTLTIPSATLEDSGTYECAVTEATNDHQDEKKIN 95

Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the Class Ib major histocompatibility complex (MHC) immunoglobulin domain of human leukocyte antigen H (HLA-H). HLA-H (also known as hereditary hemochromatosis protein; HFE) is a major histocompatibility complex (MHC) class I-like protein that is mutated in Hereditary Hemochromatosis. HFE is a protein of 343 amino acids that includes a signal peptide, an extracellular transferrin receptor-binding region (a1 and a2), an immunoglobulin-like domain (a3), a transmembrane region, and a short cytoplasmic tail. HFE binds beta-2-microglobulin to form a heterodimer expressed at the cell surface. It binds transferrin receptor (TFRC) in its extracellular alpha1-alpha2 domain. HFE plays an important part in the regulation of hepcidin expression in response to iron overload and the liver is important in the pathophysiology of HFE-associated hemochromatosis. Nine HFE splicing variants have been reported with transcripts lacking exon 2 or exon 3, or exons 2-3, 2-4, or 2-5. Diverse mutations involving HFE introns and exons discovered in persons with hemochromatosis or their family members cause or probably cause high iron phenotypes. 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 85544092 119 PP---SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERhnsYTCE 195
Cdd:cd21021   4 PPlvkVTHHVTSSVTTLRCRALNYYPQNITMKWLKDKQPMDAKEFEPKDVLPNGDGTYQGWITLAVPPGEEQR---YTCQ 80

                        90
                ....*....|.
gi 85544092 196 ATHKTSTSPIV 206
Cdd:cd21021  81 VEHPGLDQPLI 91

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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 85544092   4 MTQSQKFLSTSVGDRVSVTCKASQ--NVGTnVAWYQqkpGQSP-KPLMYSASY----RYSGVPDrfTGSGSGTDFTLTIS 76
Cdd:cd16097   2 VIQPEKSVSVAAGESATLHCTVTSliPVGP-IQWFR---GAGPgRELIYNQKEghfpRVTTVSD--LTKRNNMDFSIRIS 75

                        90       100       110
                ....*....|....*....|....*....|....*.
gi 85544092  77 NVQSEDLAEYFCQQFNRYP-----LTFGSGTKLELK 107
Cdd:cd16097  76 NITPADAGTYYCVKFRKGSpddveFKSGAGTELSVR 111

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 85544092 113 PTVSIFPPSSEQLTSGGaSVVCFLNNFYPKDINVKWKIDGSERQNGVlnSWTDQDSK-DSTYSMSSTLTLTKDEYErhnS 191
Cdd:cd21008   3 PEVTVFPKSPVTLGQPN-TLICLVDNIFPPVINITWLSNGHSVTEGV--SETSFLSKsDHSFLKISYLTFLPSADD---I 76

                        90
                ....*....|....*.
gi 85544092 192 YTCEATHKTSTSPIVK 207
Cdd:cd21008  77 YDCKVEHWGLDKPLLK 92

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 85544092  19 VSVTCKASQNVGTNVAWYqqKPGQSPKPlmysasyrysgvPDRFTGSGSGTDFTLTISNVQSEDLAEYFCQ 89
Cdd:cd00096   1 VTLTCSASGNPPPTITWY--KNGKPLPP------------SSRDSRRSELGNGTLTISNVTLEDSGTYTCV 57