NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|168988885]
View 

Chain B, Programmed cell death protein 1

Protein Classification

IgV_PD1 domain-containing protein( domain architecture ID 11610716)

IgV_PD1 domain-containing protein

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 11-122 3.20e-73

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: 213.91  E-value: 3.20e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  11 SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDT 90
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 168988885  91 RRNDSGIYLCGAISLHPKAKIEESPGAELVVT 122
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 11-122 3.20e-73

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: 213.91  E-value: 3.20e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  11 SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDT 90
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 168988885  91 RRNDSGIYLCGAISLHPKAKIEESPGAELVVT 122
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 16-122 3.48e-21

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: 81.74  E-value: 3.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885   16 PAWLTVSEGANATFTCSLSNW--SEDLMLNWNRLSPSNQ-TEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRR 92
Cdd:pfam07686   3 PREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQPPGKGpTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTL 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 168988885   93 NDSGIYLCGAIslhPKAKIEESPGAELVVT 122
Cdd:pfam07686  83 SDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 16-121 3.70e-09

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: 50.20  E-value: 3.70e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885    16 PAWLTVSEGANATFTCSLSNwSEDLMLNWNRlspsnqtekqaafsNGLSQPVQDARFQIIQlpNRHDFHMNILDTRRNDS 95
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASG-SPPPEVTWYK--------------QGGKLLAESGRFSVSR--SGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 168988885    96 GIYLCGAISlhpkAKIEESPGAELVV 121
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 11-122 3.20e-73

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: 213.91  E-value: 3.20e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  11 SLTFYPAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPSNQTEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDT 90
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 168988885  91 RRNDSGIYLCGAISLHPKAKIEESPGAELVVT 122
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 16-122 3.48e-21

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: 81.74  E-value: 3.48e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885   16 PAWLTVSEGANATFTCSLSNW--SEDLMLNWNRLSPSNQ-TEKQAAFSNGLSQPVQDARFQIIQLPNRHDFHMNILDTRR 92
Cdd:pfam07686   3 PREVTVALGGSVTLPCTYSSSmsEASTSVYWYRQPPGKGpTFLIAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLTL 82

                          90       100       110
                  ....*....|....*....|....*....|
gi 168988885   93 NDSGIYLCGAIslhPKAKIEESPGAELVVT 122
Cdd:pfam07686  83 SDSGTYTCAVI---PSGEGVFGKGTRLTVL 109
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 16-121 3.70e-09

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: 50.20  E-value: 3.70e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885    16 PAWLTVSEGANATFTCSLSNwSEDLMLNWNRlspsnqtekqaafsNGLSQPVQDARFQIIQlpNRHDFHMNILDTRRNDS 95
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASG-SPPPEVTWYK--------------QGGKLLAESGRFSVSR--SGSTSTLTISNVTPEDS 63

                           90       100
                   ....*....|....*....|....*.
gi 168988885    96 GIYLCGAISlhpkAKIEESPGAELVV 121
Cdd:smart00410  64 GTYTCAATN----SSGSASSGTTLTV 85
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 16-121 9.62e-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: 46.94  E-value: 9.62e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  16 PAWLTVSEGANATFTCSLSNWSEDLMLNWNRLSPsNQTEKQAAFSNGLSQPVQD---ARFqIIQLPNRHDFHMNILDTRR 92
Cdd:cd00099    5 PRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKP-GQGPEFLIYLSSSKGKTKGgvpGRF-SGSRDGTSSFSLTISNLQP 82

                         90       100
                 ....*....|....*....|....*....
gi 168988885  93 NDSGIYLCGAISLHPKAKIEESPGAELVV 121
Cdd:cd00099   83 EDSGTYYCAVSESGGTDKLTFGSGTRLTV 111
IgV_1_Necl_like cd05717
First (N-terminal) immunoglobulin (Ig)-like domain of the nectin-like molecules; member of the ...
 19-110 1.09e-05

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: 41.35  E-value: 1.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  19 LTVSEGANATFTCSLSNwSEDLMLNWnrLSPSNQTekqaAFSNGlSQPVQDARFQIIQLpNRHDFHMNILDTRRNDSGIY 98
Cdd:cd05717    6 VTVVEGETLTLKCQVSL-RDDSSLQW--LNPNGQT----IYFND-KRALRDSRYQLLNH-SASELSISVSNVTLSDEGVY 76

                         90
                 ....*....|..
gi 168988885  99 LCGAISLHPKAK 110
Cdd:cd05717   77 TCLHYTDPVSTK 88
IGv smart00406
Immunoglobulin V-Type;
26-100 1.47e-05

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 40.44  E-value: 1.47e-05
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 168988885    26 NATFTCSLSNWSEDLM-LNWNRLSPSNQTEKQAAFSNGLSQPVQD---ARFQIIQLPNRHDFHMNILDTRRNDSGIYLC 100
Cdd:smart00406   1 SVTLSCKFSGSTFSSYyVSWVRQPPGKGLEWLGYIGSNGSSYYQEsykGRFTISKDTSKNDVSLTISNLRVEDTGTYYC 79
IgV_1_Necl-2 cd05881
First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2; member of the ...
 19-100 6.08e-04

First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule 2; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-2, Necl-2 (also known as cell adhesion molecule 1 (CADM1), SynCAM1, IGSF4A, Tslc1, sgIGSF, and RA175). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - 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-2 has Ca(2+)-independent homophilic and heterophilic cell-cell adhesion activity. Necl-2 is expressed in a wide variety of tissues and is a putative tumour suppressor gene, which is downregulated in aggressive neuroblastoma.


Pssm-ID: 409465  Cd Length: 94  Bit Score: 36.52  E-value: 6.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  19 LTVSEGANATFTCSLSNwSEDLMLNWnrLSPSNQTEKQAAFsnglsQPVQDARFQIIQLPNrHDFHMNILDTRRNDSGIY 98
Cdd:cd05881    6 VTVVEGEVATISCRVKN-SDDSVIQL--LNPNRQTIYFRDF-----RPLKDSRFQLVNFSS-SELRVSLTNVSISDEGRY 76


                 ..
gi 168988885  99 LC 100
Cdd:cd05881   77 FC 78
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 19-100 2.07e-03

Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions.


Pssm-ID: 395002  Cd Length: 86  Bit Score: 35.25  E-value: 2.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885   19 LTVSEGANATFTCSLSNWSEDLMLNWNRlspSNQTEKqaafsngLSQPVQDARFQIIQLPnrhdfhMNILDTRRNDSGIY 98
Cdd:pfam00047   6 VTVLEGDSATLTCSASTGSPGPDVTWSK---EGGTLI-------ESLKVKHDNGRTTQSS------LLISNVTKEDAGTY 69


                  ..
gi 168988885   99 LC 100
Cdd:pfam00047  70 TC 71
IgV_1_Necl-3 cd07701
First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the ...
 19-108 4.96e-03

First (N-terminal) immunoglobulin (Ig)-like domain of nectin-like molecule-3; member of the V-set of Ig superfamily (IgSF) domains; The members here are composed of the N-terminal immunoglobulin (Ig)-like domain of nectin-like molecule-3, Necl-3 (also known as cell adhesion molecule 2 (CADM2), SynCAM2, IGSF4D). Nectin-like molecules have similar domain structures to those of nectins. At least five nectin-like molecules have been identified (Necl-1 - 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-3 accumulates in central and peripheral nervous system tissue, and has been shown to selectively interact with oligodendrocytes.


Pssm-ID: 409498  Cd Length: 96  Bit Score: 34.29  E-value: 4.96e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 168988885  19 LTVSEGANATFTCSLSNwSEDLMLNWNrlSPSNQTekqaaFSNGLSQPVQDARFQIIQlPNRHDFHMNILDTRRNDSGIY 98
Cdd:cd07701    7 VTVVEGGTANLTCRVDQ-NDNTSLQWS--NPAQQT-----LYFDDKKALRDNRIELVR-ASWHELSISISDVSLSDEGQY 77

                         90
                 ....*....|
gi 168988885  99 LCGAISLHPK 108
Cdd:cd07701   78 TCSLFTMPVK 87
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH