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Conserved domains on  [gi|830245424|ref|XP_004695897|]
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PREDICTED: programmed cell death protein 1, partial [Condylura cristata]

Protein Classification

immunoglobulin domain-containing family protein( domain architecture ID 34076)

immunoglobulin (Ig) domain-containing family protein is a member of a large superfamily containing cell surface antigen receptors, co-receptors and co-stimulatory molecules of the immune system, molecules involved in antigen presentation to lymphocytes, cell adhesion molecules, certain cytokine receptors and intracellular muscle proteins; immunoglobulin domains are typically divided into 4 main classes based on their structures and sequences: the Variable (V), Constant 1 (C1), Constant 2 (C2), and Intermediate (I) sets

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Ig super family cl11960
Immunoglobulin domain; The members here are composed of the immunoglobulin (Ig) domain found ...
 73-198 1.04e-64

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.


The actual alignment was detected with superfamily member cd16088:

Pssm-ID: 472250  Cd Length: 112  Bit Score: 196.19  E-value: 1.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  73 PPTISPARLSVPEGGNASFTCSLSHDAlptphdtqpaprdtQQARLNWYRLGPGNQSSKLAAFPEDQHQAGQDWRFRVTP 152
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTS--------------ESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQ 66

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 830245424 153 LPGGRDFLLTLVGARPHDSGTYLCVAIYLNPRVHFSESPHIKLTVT 198
Cdd:cd16088   67 LPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 73-198 1.04e-64

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


Pssm-ID: 409509  Cd Length: 112  Bit Score: 196.19  E-value: 1.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  73 PPTISPARLSVPEGGNASFTCSLSHDAlptphdtqpaprdtQQARLNWYRLGPGNQSSKLAAFPEDQHQAGQDWRFRVTP 152
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTS--------------ESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQ 66

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 830245424 153 LPGGRDFLLTLVGARPHDSGTYLCVAIYLNPRVHFSESPHIKLTVT 198
Cdd:cd16088   67 LPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 76-198 1.84e-13

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: 64.40  E-value: 1.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424   76 ISPARLSVPEGGNASFTCSLShdaLPTPHDTQpaprdtqqaRLNWYRLGPGNQSSKL-AAFPEDQHQAGQDWRFRVTPLP 154
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYS---SSMSEAST---------SVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDP 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 830245424  155 GGRDFLLTLVGARPHDSGTYLCVAIylnPRVHFSESPHIKLTVT 198
Cdd:pfam07686  69 SNGDGSLTIQNLTLSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 78-197 6.94e-07

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 45.96  E-value: 6.94e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424    78 PARLSVPEGGNASFTCSLSHDALPTphdtqpaprdtqqarLNWYRLGPgnqssKLAAFPEdqhqagqdwRFRVTPlpGGR 157
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPE---------------VTWYKQGG-----KLLAESG---------RFSVSR--SGS 49

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 830245424   158 DFLLTLVGARPHDSGTYLCVAiYLNPRVHFSEsphIKLTV 197
Cdd:smart00410  50 TSTLTISNVTPEDSGTYTCAA-TNSSGSASSG---TTLTV 85
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 73-198 1.04e-64

Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are composed of the immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1; also known as CD279/cluster of differentiation 279). PD1 is a cell surface receptor that is expressed on T cells and pro-B cells. The protein's structure includes an extracellular IgV domain followed by a transmembrane region and an intracellular tail. Activation of CD4+ T cells, CD8+ T cells, NKT cells, B cells, and monocytes induces PD-1 expression, immediately after which it binds two distinct ligands, PD-L1 (also known as B7-H1 or CD274/cluster of differentiation 274) and PD-L2, also known as B7-DC. PD-1 plays an important role in down regulating the immune system by preventing the activation of T-cells, reducing autoimmunity and promoting self-tolerance. The inhibitory effect of PD-1 is accomplished by promoting apoptosis in antigen specific T-cells in lymph nodes while simultaneously reducing apoptosis in regulatory T cells. A class of drugs that target PD-1, known as the PD-1 inhibitors, activate the immune system to attack tumors and treat cancer. Comparisons between the mouse PD-1 (mPD-1) and human PD-1 (hPD-1) reveals that unlike the mPD-1 which has a conventional IgSF V-set domain, hPD-1 lacks a C" strand, and instead the C' and D strands are connected by a long and flexible loop. In addition, the BC loop is not stabilized by disulfide bonding to the F strand of the ligand binding beta sheet. These differences result in different binding affinities of human and mouse PD-1 for their ligands.


Pssm-ID: 409509  Cd Length: 112  Bit Score: 196.19  E-value: 1.04e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  73 PPTISPARLSVPEGGNASFTCSLSHDAlptphdtqpaprdtQQARLNWYRLGPGNQSSKLAAFPEDQHQAGQDWRFRVTP 152
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTS--------------ESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQ 66

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 830245424 153 LPGGRDFLLTLVGARPHDSGTYLCVAIYLNPRVHFSESPHIKLTVT 198
Cdd:cd16088   67 LPNGRDFHMSVVRARRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 76-198 1.84e-13

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: 64.40  E-value: 1.84e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424   76 ISPARLSVPEGGNASFTCSLShdaLPTPHDTQpaprdtqqaRLNWYRLGPGNQSSKL-AAFPEDQHQAGQDWRFRVTPLP 154
Cdd:pfam07686   1 QTPREVTVALGGSVTLPCTYS---SSMSEAST---------SVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDP 68

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 830245424  155 GGRDFLLTLVGARPHDSGTYLCVAIylnPRVHFSESPHIKLTVT 198
Cdd:pfam07686  69 SNGDGSLTIQNLTLSDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 75-180 1.18e-08

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: 51.57  E-value: 1.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  75 TISPARLSVPEGGNASFTCSLShDALPTPhdtqpaprdtqqaRLNWYRLGPGNQSSKLA--AFPEDQHQAGQDWRFRVTp 152
Cdd:cd00099    2 TQSPRSLSVQEGESVTLSCEVS-SSFSST-------------YIYWYRQKPGQGPEFLIylSSSKGKTKGGVPGRFSGS- 66

                         90       100
                 ....*....|....*....|....*...
gi 830245424 153 LPGGRDFLLTLVGARPHDSGTYLCVAIY 180
Cdd:cd00099   67 RDGTSSFSLTISNLQPEDSGTYYCAVSE 94
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 78-197 6.94e-07

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


Pssm-ID: 214653 [Multi-domain]  Cd Length: 85  Bit Score: 45.96  E-value: 6.94e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424    78 PARLSVPEGGNASFTCSLSHDALPTphdtqpaprdtqqarLNWYRLGPgnqssKLAAFPEdqhqagqdwRFRVTPlpGGR 157
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPE---------------VTWYKQGG-----KLLAESG---------RFSVSR--SGS 49

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|
gi 830245424   158 DFLLTLVGARPHDSGTYLCVAiYLNPRVHFSEsphIKLTV 197
Cdd:smart00410  50 TSTLTISNVTPEDSGTYTCAA-TNSSGSASSG---TTLTV 85
IGv smart00406
Immunoglobulin V-Type;
88-176 6.74e-06

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 43.14  E-value: 6.74e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424    88 NASFTCSLSHDALPTPHdtqpaprdtqqarLNWYRLGPGNQSSKLAAFPEDQHQAGQDW---RFRVTPLPGGRDFLLTLV 164
Cdd:smart00406   1 SVTLSCKFSGSTFSSYY-------------VSWVRQPPGKGLEWLGYIGSNGSSYYQESykgRFTISKDTSKNDVSLTIS 67

                           90
                   ....*....|..
gi 830245424   165 GARPHDSGTYLC 176
Cdd:smart00406  68 NLRVEDTGTYYC 79
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 75-177 1.62e-05

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.


Pssm-ID: 409369  Cd Length: 106  Bit Score: 42.76  E-value: 1.62e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  75 TISPARLSVPEGGNASFTCSLSHDALPTphdtqpaprdtqqaRLNWYRLGPGnQSSKLAAFPEDQHQAGQDWRFRVTPlp 154
Cdd:cd04980    4 TQSPASLSVSPGERVTISCKASQSISSN--------------YLAWYQQKPG-QAPKLLIYYASTLHSGVPSRFSGSG-- 66

                         90       100
                 ....*....|....*....|...
gi 830245424 155 GGRDFLLTLVGARPHDSGTYLCV 177
Cdd:cd04980   67 SGTDFTLTISSVEPEDAAVYYCQ 89
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 73-178 1.05e-04

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 39.47  E-value: 1.05e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424   73 PPTI--SPARLSVPEGGNASFTCSLSHDalPTPHDTqpaprdtqqarlnWYRLGPGNQSSKLAAFPEDQHQAgqdwrfrv 150
Cdd:pfam13927   1 KPVItvSPSSVTVREGETVTLTCEATGS--PPPTIT-------------WYKNGEPISSGSTRSRSLSGSNS-------- 57

                          90       100
                  ....*....|....*....|....*...
gi 830245424  151 tplpggrdfLLTLVGARPHDSGTYLCVA 178
Cdd:pfam13927  58 ---------TLTISNVTRSDAGTYTCVA 76
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 77-178 3.97e-04

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.


Pssm-ID: 409372 [Multi-domain]  Cd Length: 109  Bit Score: 38.79  E-value: 3.97e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 830245424  77 SPARLSVPEGGNASFTCSlshdalptpHDTQPAPRdtqqarLNWYRLGPGNQ-SSKLAAFPEDQHQagQDWRFRVTPLPG 155
Cdd:cd04983    4 SPQSLSVQEGENVTLNCN---------YSTSTFYY------LFWYRQYPGQGpQFLIYISSDSGNK--KKGRFSATLDKS 66

                         90       100
                 ....*....|....*....|...
gi 830245424 156 GRDFLLTLVGARPHDSGTYLCVA 178
Cdd:cd04983   67 RKSSSLHISAAQLSDSAVYFCAL 89
 
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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