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Conserved domains on  [gi|18088256|gb|AAH20568|]
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Chromosome 10 open reading frame 54 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
IgV_VISTA cd20980
Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell ...
 34-181 4.91e-106

Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA); The members here are composed of the immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA; also known as B7-H5, PD-1H, Gi24, Dies1, SISP1 and DD1alpha). VISTA is an immune checkpoint protein involved in the regulation of T cell activity and inhibits the T cell response against cancer. VISTA is a type I transmembrane protein with a single IgV domain with sequence homology to the IgV domains of the members of B7 family. VISTA is the only B7 family member that lacks an IgC domain. VISTA is primarily expressed in white blood cells and its transcription is partially controlled by p53. Similar to PD-1/PD-L1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Unlike the B7 family members, VISTA contains 10 beta-strands, instead of the nine that typically comprises of an IgV fold. Moreover, human VISTA contains the 21-residue extended loop between stands C and C', which does not align with any B7 family structure.


:

Pssm-ID: 409572  Cd Length: 147  Bit Score: 305.31  E-value: 4.91e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  34 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGHQAaNTSHDL 113
Cdd:cd20980   1 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGQAA-NTSHDL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18088256 114 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEHRVHGAMELQVQTGKDAPSNCVVY 181
Cdd:cd20980  80 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEQRLYGAMELQVQTGKDAPSTCVAY 147
 
Name Accession Description Interval E-value
IgV_VISTA cd20980
Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell ...
 34-181 4.91e-106

Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA); The members here are composed of the immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA; also known as B7-H5, PD-1H, Gi24, Dies1, SISP1 and DD1alpha). VISTA is an immune checkpoint protein involved in the regulation of T cell activity and inhibits the T cell response against cancer. VISTA is a type I transmembrane protein with a single IgV domain with sequence homology to the IgV domains of the members of B7 family. VISTA is the only B7 family member that lacks an IgC domain. VISTA is primarily expressed in white blood cells and its transcription is partially controlled by p53. Similar to PD-1/PD-L1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Unlike the B7 family members, VISTA contains 10 beta-strands, instead of the nine that typically comprises of an IgV fold. Moreover, human VISTA contains the 21-residue extended loop between stands C and C', which does not align with any B7 family structure.


Pssm-ID: 409572  Cd Length: 147  Bit Score: 305.31  E-value: 4.91e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  34 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGHQAaNTSHDL 113
Cdd:cd20980   1 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGQAA-NTSHDL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18088256 114 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEHRVHGAMELQVQTGKDAPSNCVVY 181
Cdd:cd20980  80 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEQRLYGAMELQVQTGKDAPSTCVAY 147
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 37-161 2.71e-08

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 50.92  E-value: 2.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256    37 TPYSLYVcPEGQNVTLTCRLLGPVDKGHdvtFYKTWYRSSRGEVQTCSerrpirnLTFQDLHLHHGGHQAANTSHDLAQR 116
Cdd:pfam07686   2 TPREVTV-ALGGSVTLPCTYSSSMSEAS---TSVYWYRQPPGKGPTFL-------IAYYSNGSEEGVKKGRFSGRGDPSN 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 18088256   117 hglesasdhhGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEHRVH 161
Cdd:pfam07686  71 ----------GDGSLTIQNLTLSDSGTYTCAVIPSGEGVFGKGTR 105
 
Name Accession Description Interval E-value
IgV_VISTA cd20980
Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell ...
 34-181 4.91e-106

Immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA); The members here are composed of the immunoglobulin variable (IgV) domain of V-domain immunoglobulin suppressor of T cell activation (VISTA; also known as B7-H5, PD-1H, Gi24, Dies1, SISP1 and DD1alpha). VISTA is an immune checkpoint protein involved in the regulation of T cell activity and inhibits the T cell response against cancer. VISTA is a type I transmembrane protein with a single IgV domain with sequence homology to the IgV domains of the members of B7 family. VISTA is the only B7 family member that lacks an IgC domain. VISTA is primarily expressed in white blood cells and its transcription is partially controlled by p53. Similar to PD-1/PD-L1 and CTLA-4, a blockade of VISTA promotes tumor clearance by the immune system. Unlike the B7 family members, VISTA contains 10 beta-strands, instead of the nine that typically comprises of an IgV fold. Moreover, human VISTA contains the 21-residue extended loop between stands C and C', which does not align with any B7 family structure.


Pssm-ID: 409572  Cd Length: 147  Bit Score: 305.31  E-value: 4.91e-106
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  34 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGHQAaNTSHDL 113
Cdd:cd20980   1 KVATPYSLYVCPEGQNVTLTCRLLGPVDKGHDVTFYKTWYRSSRGEVQTCSERRPIRNLTFQDLHLHHGGQAA-NTSHDL 79

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18088256 114 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEHRVHGAMELQVQTGKDAPSNCVVY 181
Cdd:cd20980  80 AQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEQRLYGAMELQVQTGKDAPSTCVAY 147
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 37-161 2.71e-08

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


Pssm-ID: 462230  Cd Length: 109  Bit Score: 50.92  E-value: 2.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256    37 TPYSLYVcPEGQNVTLTCRLLGPVDKGHdvtFYKTWYRSSRGEVQTCSerrpirnLTFQDLHLHHGGHQAANTSHDLAQR 116
Cdd:pfam07686   2 TPREVTV-ALGGSVTLPCTYSSSMSEAS---TSVYWYRQPPGKGPTFL-------IAYYSNGSEEGVKKGRFSGRGDPSN 70

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 18088256   117 hglesasdhhGNFSITMRNLTLLDSGLYCCLVVEIRHHHSEHRVH 161
Cdd:pfam07686  71 ----------GDGSLTIQNLTLSDSGTYTCAVIPSGEGVFGKGTR 105
IgV_PDl1 cd20947
Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here ...
 35-148 1.06e-04

Immunoglobulin Variable (IgV) domain of Programmed death ligand 1 (PD-L1); The members here are composed of the immunoglobulin variable (IgV) domain of Programmed death ligand 1 (PD-L1; also known as Cluster of Differentiation 274 (CD274)). PD-L1 is a cell-surface ligand that competes with PD-L2 for binding to the immunosuppressive receptor programmed death-1 (PD-1). PD-1 is a member of the B7 family that plays an important role in negatively regulating immune responses upon interaction with its two ligands, PD-L1 or PD-L2. Like PD-L2, PD-L1 interacts with PD-1 and suppresses T cell proliferation and cytokine production. The PD-1 receptor is expressed on the surface of activated T cells, while PD-L1 is expressed on cancer cells. When PD-1 and PD-L1 bind together, they form a molecular shield protecting tumor cells from being destroyed by the immune system. Thus, inhibiting the binding of PD-L1 to PD-1 with an antibody leads to killing of tumor cells by T cells. PD-1 inhibitors (such as Pembrolizumab, Nivolumab, and Cemiplimab) and PD-L1 inhibitors (such as Atezolizumab, Avelumab, and Durvalumab ) are an emerging class of immunotherapy that stimulate lymphocytes against tumor cells.


Pssm-ID: 409539  Cd Length: 110  Bit Score: 41.07  E-value: 1.06e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  35 VATPYSLYVCPEGQNVTLTCRLlgPVDKGHDVT-FYKTWYRSSRGEVQTCSERrpirnltfQDLHLHHGGHQaantshdl 113
Cdd:cd20947   1 VTVPKDLYVVEYGSNMTIECKF--PVEKQLDLAaLIVYWEMEDKNIIQFVHGE--------EDLKVQHSSYR-------- 62

                        90       100       110
                ....*....|....*....|....*....|....*
gi 18088256 114 aQRHGLESASDHHGNFSITMRNLTLLDSGLYCCLV 148
Cdd:cd20947  63 -QRARLLKDQLSLGNAALQITDVKLQDAGVYRCMI 96
IgV_TIM-3_like cd20982
Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3) ...
 42-151 6.95e-04

Immunoglobulin Variable (IgV) domain of T cell Immunoglobulin Domain and Mucin Domain 3 (Tim-3), and similar domains; The members here are composed of the immunoglobulin variable (IgV) domain of T cell immunoglobulin domain and mucin domain 3 (Tim-3; also known as Hepatitis A virus cellular receptor 2 (HAVcr-2) and Cluster of Differentiation 366 (CD366)) and similar proteins. TIM-3 is a checkpoint inhibitor in immune responses to tumors, as well as involved in chronic viral infections. Thus, Tim-3 has emerged as one of most promising immune checkpoint targets for cancer immunotherapy. Tim-3 is highly expressed on Th1 lymphocytes and CD11b(+) macrophages and is upregulated on activated T and myeloid cells. TIM-3 regulates macrophage, activation and inhibits Th1 mediated immune responses to promote immunological tolerance. There are three TIM family members in humans (TIM-1, TIM-3, and TIM-4) and eight members in mice (TIM-1 to TIM-8). The IgV domain of human TIM-3 has been shown to bind ligands such as carcinoembryonic antigen cell adhesion molecule 1 (CEACAM1), high mobility group protein B1 (HMGB1)and galectin-9 (GAL9). The binding of GAL9 to TIM-3 can negatively regulate Th1 immune response, enhance immune tolerance and inhibit anti#tumor immunity. Dysregulation of the TIM-3/GAL9 pathway is implicated in numerous chronic autoimmune diseases, such as multiple sclerosis and systemic lupus erythematosus.


Pssm-ID: 409574  Cd Length: 107  Bit Score: 38.59  E-value: 6.95e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  42 YVCPEGQNVTLTCrllgpvdkghdvtFYKTWYRSsrGEVQTCSERRPIRNLTFQDLHLHHGGHqaaNTSHDLAQRHGLEs 121
Cdd:cd20982   3 YRAEVGHNAYLPC-------------SYTTAAPG--NLVPVCWGKGACPVSYCGNVLLRTDER---DVTYQKSSRYQLK- 63

                        90       100       110
                ....*....|....*....|....*....|
gi 18088256 122 ASDHHGNFSITMRNLTLLDSGLYCClVVEI 151
Cdd:cd20982  64 GDFSKGDVSLTIENVTLADSGIYCC-RIQI 92
IgV_pIgR_like cd05716
Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The ...
 126-158 8.54e-04

Immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins; The members here are composed of the immunoglobulin (Ig)-like domain in the polymeric Ig receptor (pIgR) and similar proteins. pIgR delivers dimeric IgA and pentameric IgM to mucosal secretions. Polymeric immunoglobulin (pIgs) are the first defense against pathogens and toxins. IgA and IgM can form polymers via an 18-residue extension at their C-termini referred to as the tailpiece. pIgR transports pIgs across mucosal epithelia into mucosal secretions. Human pIgR is a glycosylated type I transmembrane protein, comprised of a 620-residue extracellular region, a 23-residue transmembrane region, and a 103-residue cytoplasmic tail. The extracellular region contains five domains that share sequence similarity with Ig variable (v) regions. This group also contains the Ig-like extracellular domains of other receptors such as NK cell receptor Nkp44 and myeloid receptors, among others.


Pssm-ID: 409381  Cd Length: 100  Bit Score: 38.15  E-value: 8.54e-04
                        10        20        30
                ....*....|....*....|....*....|...
gi 18088256 126 HGNFSITMRNLTLLDSGLYCClVVEIRHHHSEH 158
Cdd:cd05716  63 NGVFTVTLNQLRKEDAGWYWC-GVGDDGDRGLT 94
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 37-146 9.70e-04

Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here are composed of the immunoglobulin (Ig) variable domain of the beta 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 includes the variable domain of the alpha chain of alpha/beta 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.


Pssm-ID: 409480  Cd Length: 110  Bit Score: 38.03  E-value: 9.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  37 TPySLYVCPEGQNVTLTCRLlgpvDKGHDVTFyktWYRSSRGEvqtcserrpirnlTFQDLHLHHGGHQAAN----TSHD 112
Cdd:cd05899   4 SP-RYLIKRRGQSVTLRCSQ----KSGHDNMY---WYRQDPGK-------------GLQLLFYSYGGGLNEEgdlpGDRF 62

                        90       100       110
                ....*....|....*....|....*....|....
gi 18088256 113 LAQRHGLEsasdhhgNFSITMRNLTLLDSGLYCC 146
Cdd:cd05899  63 SASRPSLT-------RSSLTIKSAEPEDSAVYLC 89
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 37-150 1.97e-03

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.


Pssm-ID: 409355 [Multi-domain]  Cd Length: 111  Bit Score: 37.31  E-value: 1.97e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  37 TPYSLyVCPEGQNVTLTCRLLGPVdkGHDVTFyktWYRSSRGEvqtcserrpirNLTFqdlhLHHGGHQAANTSHDLAQR 116
Cdd:cd00099   4 SPRSL-SVQEGESVTLSCEVSSSF--SSTYIY---WYRQKPGQ-----------GPEF----LIYLSSSKGKTKGGVPGR 62

                        90       100       110
                ....*....|....*....|....*....|....*
gi 18088256 117 hglESASDHHGN-FSITMRNLTLLDSGLYCCLVVE 150
Cdd:cd00099  63 ---FSGSRDGTSsFSLTISNLQPEDSGTYYCAVSE 94
IgV_1_Necl_like cd05717
First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the ...
 46-147 3.36e-03

First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of the nectin-like molecules Necl-1 (also known as cell adhesion molecule 3 (CADM3)), Necl-2 (CADM1), Necl-3 (CADM2), and similar proteins. At least five nectin-like molecules have been identified (Necl-1 to Necl-5). They all have an extracellular region containing three Ig-like domains, a transmembrane region, and a cytoplasmic region. The N-terminal Ig-like domain of the extracellular region belongs to the V-type subfamily of Ig domains, is essential to cell-cell adhesion, and plays a part in the interaction with the envelope glycoprotein D of various viruses. Necl-1, Necl-2, and Necl-3 have Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-1 is specifically expressed in neural tissue, and is important to the formation of synapses, axon bundles, and myelinated axons. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene which is downregulated in aggressive neuroblastoma. Necl-3 accumulates in central and peripheral nervous system tissue and has been shown to selectively interact with oligodendrocytes. This group also contains Class-I MHC-restricted T-cell-associated molecule (CRTAM), whose expression pattern is consistent with its expression in Class-I MHC-restricted T-cells.


Pssm-ID: 409382  Cd Length: 94  Bit Score: 36.34  E-value: 3.36e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18088256  46 EGQNVTLTCRllgpVDKGHDVTFykTWYRSSrGEVQTCSERRPIRNLTFQDLHLhhgghqaanTSHDLaqrhglesasdh 125
Cdd:cd05717  10 EGETLTLKCQ----VSLRDDSSL--QWLNPN-GQTIYFNDKRALRDSRYQLLNH---------SASEL------------ 61

                        90       100
                ....*....|....*....|..
gi 18088256 126 hgnfSITMRNLTLLDSGLYCCL 147
Cdd:cd05717  62 ----SISVSNVTLSDEGVYTCL 79
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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