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

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27436893 292 PKVSLmpaTLARAAPGEAPPELLCLVSHFYPSGgLEVEWELRGGPGGRSQKAEGQRWLSALRHHSDGSVSLSGHLQPPPv 371
Cdd:cd05771   1 PRVRL---SPKNLVKPDLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 27436893 372 TTEQHGARYACRIHHPSLPA 391
Cdd:cd05771  76 GTENRGATYTCRVTHVSLEE 95

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 27436893 292 PKVSLmpaTLARAAPGEAPPELLCLVSHFYPSGgLEVEWELRGGPGGRSQKAEGQRWLSALRHHSDGSVSLSGHLQPPPv 371
Cdd:cd05771   1 PRVRL---SPKNLVKPDLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 27436893 372 TTEQHGARYACRIHHPSLPA 391
Cdd:cd05771  76 GTENRGATYTCRVTHVSLEE 95

Immunoglobulin C-Type;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 27436893    313 LLCLVSHFYPSgGLEVEWELRGGPggRSQKAEgqrwLSALRHHSDGSVSLSGHLQPPPVTTEQHgARYACRIHHPSLP 390
Cdd:smart00407   4 LVCLVSGFYPP-DITVTWLRNGQE--VTEGVS----TTDPLKNSDGTYFLSSYLTVPASTWESG-DVYTCQVTHEGLK 73

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 27436893 292 PKVSLmpaTLARAAPGEAPPELLCLVSHFYPSGgLEVEWELRGGPGGRSQKAEGQRWLSALRHHSDGSVSLSGHLQPPPv 371
Cdd:cd05771   1 PRVRL---SPKNLVKPDLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 27436893 372 TTEQHGARYACRIHHPSLPA 391
Cdd:cd05771  76 GTENRGATYTCRVTHVSLEE 95

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27436893   310 PPELLCLVSHFYPsGGLEVEWELRGGPggRSQKAEgqrwLSALRHHSDGSVSLSGHLQPPPVTTEQhGARYACRIHHPSL 389
Cdd:pfam07654  14 PNTLTCLVTGFYP-PDITVTWLKNGQE--VTEGVK----TTPPSPNSDWTYQLSSYLTVTPSDWES-GDEYTCRVEHEGL 85

Immunoglobulin light chain Constant domain; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin (Ig) light chain constant (C) domain. 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 determine the type of immunoglobulin: 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 27436893 291 PPKVSLMPATLARAAPGEAppELLCLVSHFYPsGGLEVEWELRGGP---GGRSQKAEGQrwlsalrhhSDGSVSLSGHLQ 367
Cdd:cd07699   1 APSVTIFPPSSEELSSGKA--TLVCLINKFYP-GFATVTWKVDGSTvssGVTTSKTEQQ---------SDNTYSMSSYLT 68

                        90       100
                ....*....|....*....|....*
gi 27436893 368 PPPVTTEQHgARYACRIHHPSLPAS 392
Cdd:cd07699  69 LSSSDWNKH-KVYTCEVTHEGLSST 92

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 27436893 290 KPPKVSLMpatlARAAPGEAPPELLCLVSHFYPSgGLEVEWeLRggpGGRSQKAEGQRwlSALRHHSDGSVSLSGHLQPP 369
Cdd:cd21029   1 VKPRVRLS----SRPSPGDGHLQLSCHVTGFYPR-PIEVTW-LR---DGQEQMDGTQS--GGILPNHDGTYQLRKTLDIA 69

                        90       100
                ....*....|....*....|.
gi 27436893 370 PvtteQHGARYACRIHHPSLP 390
Cdd:cd21029  70 P----GEGAGYSCRVDHSSLK 86

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 27436893 292 PKVSLMPAtlaRAAPGEAPPELLCLVSHFYPsGGLEVEWeLRGGPGGRSQKAEgqrwlSALRHHSDGSVSLSGHLQPPPv 371
Cdd:cd20998   7 PTVTVYPT---KTQPLEHHNLLVCSVSDFYP-GNIEVRW-FRNGKEEKTGIVS-----TGLVRNGDWTFQTLVMLETVP- 75

                        90
                ....*....|....*...
gi 27436893 372 tteQHGARYACRIHHPSL 389
Cdd:cd20998  76 ---QSGEVYTCQVEHPSL 90

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 27436893 291 PPKVSLMPAtlaRAAPGEAPPELLCLVSHFYPsGGLEVEWELRGgpggrsQKAEGQRWLSALRHHSDGSVSLSGHLQPPP 370
Cdd:cd21003   3 QPKVNVSPS---KKGPLQHHNLLVCHVTDFYP-GNIQVRWFLNG------QEETAGVVSTNLIHNGDWTFQILVMLEMTP 72

                        90
                ....*....|....*....
gi 27436893 371 vtteQHGARYACRIHHPSL 389
Cdd:cd21003  73 ----QQGDVYTCQVEHPSL 87