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 16975494 294 PRVSLTPAPIVWAapgEAPPELLCLVSHFYPEEgLEVEWELRGGPEGSSRKAEGKTWVSTVRHHSDGSVSQSGHLQLPPv 373
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 16975494 374 TDKQHGVRYACRVRHPSLPS 393
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 16975494 294 PRVSLTPAPIVWAapgEAPPELLCLVSHFYPEEgLEVEWELRGGPEGSSRKAEGKTWVSTVRHHSDGSVSQSGHLQLPPv 373
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 16975494 374 TDKQHGVRYACRVRHPSLPS 393
Cdd:cd05771  76 GTENRGATYTCRVTHVSLEE 95

Immunoglobulin C-Type;

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16975494    315 LLCLVSHFYPEEgLEVEWELRGGP--EGSSRkaegktwvSTVRHHSDGSVSQSGHLQLPPVTDKQHGVrYACRVRHPSLP 392
Cdd:smart00407   4 LVCLVSGFYPPD-ITVTWLRNGQEvtEGVST--------TDPLKNSDGTYFLSSYLTVPASTWESGDV-YTCQVTHEGLK 73

                   .
gi 16975494    393 S 393
Cdd:smart00407  74 E 74

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 16975494 294 PRVSLTPAPIVWAapgEAPPELLCLVSHFYPEEgLEVEWELRGGPEGSSRKAEGKTWVSTVRHHSDGSVSQSGHLQLPPv 373
Cdd:cd05771   1 PRVRLSPKNLVKP---DLPQTLSCHIAGYYPLD-VDVEWLREEPGGSESQVSRDGVSLSSHRQSVDGTYSISSYLTLEP- 75

                        90       100
                ....*....|....*....|
gi 16975494 374 TDKQHGVRYACRVRHPSLPS 393
Cdd:cd05771  76 GTENRGATYTCRVTHVSLEE 95

Immunoglobulin C1-set domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16975494   312 PPELLCLVSHFYPEEgLEVEWELRGGPEGSSRKaegktwVSTVRHHSDGSVSQSGHLQLPPVTDKQHGVrYACRVRHPSL 391
Cdd:pfam07654  14 PNTLTCLVTGFYPPD-ITVTWLKNGQEVTEGVK------TTPPSPNSDWTYQLSSYLTVTPSDWESGDE-YTCRVEHEGL 85

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 16975494 292 KPPRVSLTPAPivwaAPGEAPPELLCLVSHFYPEEgLEVEWeLRGGPEGSSRKAEGktwvsTVRHHSDGSVSQSGHLQLP 371
Cdd:cd21029   1 VKPRVRLSSRP----SPGDGHLQLSCHVTGFYPRP-IEVTW-LRDGQEQMDGTQSG-----GILPNHDGTYQLRKTLDIA 69

                        90       100
                ....*....|....*....|.
gi 16975494 372 PvtDKQHGvrYACRVRHPSLP 392
Cdd:cd21029  70 P--GEGAG--YSCRVDHSSLK 86

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 16975494 293 PPRVSLTPAPIVWAAPGEAppELLCLVSHFYPeEGLEVEWELrggpEGSSRKAEGKTwvSTVRHHSDGSVSQSGHLQLPP 372
Cdd:cd07699   1 APSVTIFPPSSEELSSGKA--TLVCLINKFYP-GFATVTWKV----DGSTVSSGVTT--SKTEQQSDNTYSMSSYLTLSS 71

                        90       100
                ....*....|....*....|..
gi 16975494 373 VTDKQHGVrYACRVRHPSLPSS 394
Cdd:cd07699  72 SDWNKHKV-YTCEVTHEGLSST 92

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 16975494 314 ELLCLVSHFYPEEgLEVEWELRG------GPEGSSRKAEGKTWvSTvrhHSDGSVSQsghlqlppvTDKQHGVRYACRVR 387
Cdd:cd05847  20 QLLCLISGYTPST-IEVEWLVDGqvatlsAASTAPQKEEGGTF-ST---TSKLNVTQ---------EDWKSGKTYTCKVT 85

                ..
gi 16975494 388 HP 389
Cdd:cd05847  86 HQ 87

Class I major histocompatibility complex (MHC) beta-2-microglobulin; member of the C1-set of Ig superfamily (IgSF) domains; The members here are composed of the immunoglobulin-like domain in beta-2-microglobulin (beta2m). Beta2m is the non-covalently bound light chain of the human class I major histocompatibility complex (MHC-I). Beta2m is structured as a beta-sandwich domain composed of two facing beta-sheets (four stranded and three stranded), that is typical of the C-type immunoglobulin superfamily. This structure is stabilized by an intramolecular disulfide bridge connecting two Cys residues in the facing beta-sheets. In vivo, MHC-I continuously exposes beta2m on the cell surface, where it may be released to plasmatic fluids, transported to the kidneys, degraded, and finally excreted.

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 16975494 298 LTPAPIVWAA-PGEA--PPELLCLVSHFYPEEgLEVEWELRGGPegsSRKAEgktwvstvrhHSDGSVSQSGHLQLPPVT 374
Cdd:cd05770   1 STPKVQVYSRfPAENgkPNVLNCYVSGFHPPD-IEIRLLKNGVK---IEDVE----------QSDLSFSKDWTFYLLKYT 66

                        90
                ....*....|....*....
gi 16975494 375 D--KQHGVRYACRVRHPSL 391
Cdd:cd05770  67 EftPTKGDEYACRVRHNTL 85

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 16975494 293 PPRVSLTPAPivwAAPGEAPPELLCLVSHFYPEEgLEVEWELRGGPEGSSRkaegktwVST-VRHHSDGSVSQSGHLQLP 371
Cdd:cd21003   3 QPKVNVSPSK---KGPLQHHNLLVCHVTDFYPGN-IQVRWFLNGQEETAGV-------VSTnLIHNGDWTFQILVMLEMT 71

                        90       100
                ....*....|....*....|..
gi 16975494 372 PvtdkQHGVRYACRVRHPSLPS 393
Cdd:cd21003  72 P----QQGDVYTCQVEHPSLDS 89