NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|167857792|ref|NP_005009|]
View 

programmed cell death protein 1 precursor [Homo sapiens]

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 ...
 34-145 1.13e-79

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: 236.25  E-value: 1.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  34 PPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 167857792 114 RRNDSGTYLCGAISLAPKAQIKESLRAELRVT 145
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 ...
 34-145 1.13e-79

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: 236.25  E-value: 1.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  34 PPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 167857792 114 RRNDSGTYLCGAISLAPKAQIKESLRAELRVT 145
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-127 5.14e-14

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: 66.71  E-value: 5.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792   38 SPALLVVTEGDNATFTCSFSN--TSESFVLNWYRMSPSNQTDKL-AAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRAR 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmSEASTSVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90
                  ....*....|...
gi 167857792  115 RNDSGTYLCGAIS 127
Cdd:pfam07686  82 LSDSGTYTCAVIP 94
IGv smart00406
Immunoglobulin V-Type;
49-123 5.93e-10

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 54.70  E-value: 5.93e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167857792    49 NATFTCSFS-NTSESFVLNWYRMSPSNQTDKLAAFP-EDRSQPGQDCRFRVTQL--PNGRDFHMSVVRARRNDSGTYLC 123
Cdd:smart00406   1 SVTLSCKFSgSTFSSYYVSWVRQPPGKGLEWLGYIGsNGSSYYQESYKGRFTISkdTSKNDVSLTISNLRVEDTGTYYC 79
 
Name Accession Description Interval E-value
IgV_PD1 cd16088
Immunoglobulin (Ig)-like domain of Programmed Cell Death 1 (PD1); The members here are ...
 34-145 1.13e-79

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: 236.25  E-value: 1.13e-79
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  34 PPTFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTDKLAAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRA 113
Cdd:cd16088    1 PPTFSPALLVVTEGANATFTCSFSNTSESFVLNWYRLSPSNQTDKLAAFPEDRSQPGQDWRFRVTQLPNGRDFHMSVVRA 80

                         90       100       110
                 ....*....|....*....|....*....|..
gi 167857792 114 RRNDSGTYLCGAISLAPKAQIKESLRAELRVT 145
Cdd:cd16088   81 RRNDSGTYLCGAISLAPKAQIKESPRAELRVT 112
V-set pfam07686
Immunoglobulin V-set domain; This domain is found in antibodies as well as neural protein P0 ...
 38-127 5.14e-14

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: 66.71  E-value: 5.14e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792   38 SPALLVVTEGDNATFTCSFSN--TSESFVLNWYRMSPSNQTDKL-AAFPEDRSQPGQDCRFRVTQLPNGRDFHMSVVRAR 114
Cdd:pfam07686   2 TPREVTVALGGSVTLPCTYSSsmSEASTSVYWYRQPPGKGPTFLiAYYSNGSEEGVKKGRFSGRGDPSNGDGSLTIQNLT 81

                          90
                  ....*....|...
gi 167857792  115 RNDSGTYLCGAIS 127
Cdd:pfam07686  82 LSDSGTYTCAVIP 94
IGv smart00406
Immunoglobulin V-Type;
49-123 5.93e-10

Immunoglobulin V-Type;


Pssm-ID: 214650  Cd Length: 81  Bit Score: 54.70  E-value: 5.93e-10
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 167857792    49 NATFTCSFS-NTSESFVLNWYRMSPSNQTDKLAAFP-EDRSQPGQDCRFRVTQL--PNGRDFHMSVVRARRNDSGTYLC 123
Cdd:smart00406   1 SVTLSCKFSgSTFSSYYVSWVRQPPGKGLEWLGYIGsNGSSYYQESYKGRFTISkdTSKNDVSLTISNLRVEDTGTYYC 79
IgV cd00099
Immunoglobulin variable domain (IgV); The members here are composed of the immunoglobulin ...
 36-123 3.61e-09

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: 53.49  E-value: 3.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  36 TFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQtdklaafPE---------DRSQPGQDCRFRVTqLPNGRDF 106
Cdd:cd00099    2 TQSPRSLSVQEGESVTLSCEVSSSFSSTYIYWYRQKPGQG-------PEfliylssskGKTKGGVPGRFSGS-RDGTSSF 73

                         90
                 ....*....|....*..
gi 167857792 107 HMSVVRARRNDSGTYLC 123
Cdd:cd00099   74 SLTISNLQPEDSGTYYC 90
IG_like smart00410
Immunoglobulin like; IG domains that cannot be classified into one of IGv1, IGc1, IGc2, IG.
 39-125 1.09e-08

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: 51.35  E-value: 1.09e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792    39 PALLVVTEGDNATFTCSFSNTSESFVlNWYRmspsnQTDKLAAFPEdrsqpgqdcRFRVTQlpNGRDFHMSVVRARRNDS 118
Cdd:smart00410   1 PPSVTVKEGESVTLSCEASGSPPPEV-TWYK-----QGGKLLAESG---------RFSVSR--SGSTSTLTISNVTPEDS 63


                   ....*..
gi 167857792   119 GTYLCGA 125
Cdd:smart00410  64 GTYTCAA 70
IgV_L_kappa cd04980
Immunoglobulin (Ig) light chain, kappa type, variable (V) domain; The members here are ...
 36-123 1.73e-07

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: 48.54  E-value: 1.73e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  36 TFSPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPsNQTDKLAAFPEDRSQPGQDCRFRVTQlpNGRDFHMSVVRARR 115
Cdd:cd04980    4 TQSPASLSVSPGERVTISCKASQSISSNYLAWYQQKP-GQAPKLLIYYASTLHSGVPSRFSGSG--SGTDFTLTISSVEP 80


                 ....*...
gi 167857792 116 NDSGTYLC 123
Cdd:cd04980   81 EDAAVYYC 88
IgV_TCR_alpha cd04983
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar ...
 38-123 5.63e-07

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: 47.27  E-value: 5.63e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  38 SPALLVVTEGDNATFTCSFSNTSESFVLnWYRMSPSNQtdklaafPE------DRSQPGQDCRFRVTQLPNGRDFHMSVV 111
Cdd:cd04983    4 SPQSLSVQEGENVTLNCNYSTSTFYYLF-WYRQYPGQG-------PQfliyisSDSGNKKKGRFSATLDKSRKSSSLHIS 75

                         90
                 ....*....|..
gi 167857792 112 RARRNDSGTYLC 123
Cdd:cd04983   76 AAQLSDSAVYFC 87
ig pfam00047
Immunoglobulin domain; Members of the immunoglobulin superfamily are found in hundreds of ...
 38-123 2.57e-05

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: 41.80  E-value: 2.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792   38 SPALLVVTEGDNATFTCSFSNTSESFVLNWYRMSPSNQTdklaafpEDRSQPGQDcRFRVTQLpngrdfhmSVVRARRND 117
Cdd:pfam00047   2 APPTVTVLEGDSATLTCSASTGSPGPDVTWSKEGGTLIE-------SLKVKHDNG-RTTQSSL--------LISNVTKED 65


                  ....*.
gi 167857792  118 SGTYLC 123
Cdd:pfam00047  66 AGTYTC 71
Ig_3 pfam13927
Immunoglobulin domain; This family contains immunoglobulin-like domains.
 34-125 1.86e-03

Immunoglobulin domain; This family contains immunoglobulin-like domains.


Pssm-ID: 464046 [Multi-domain]  Cd Length: 78  Bit Score: 36.39  E-value: 1.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792   34 PP--TFSPALLVVTEGDNATFTCSFSNTSESFVLnWYRmspsnqtdklaafpEDRSQPGQDCRFRVTQLPNGRdfhMSVV 111
Cdd:pfam13927   1 KPviTVSPSSVTVREGETVTLTCEATGSPPPTIT-WYK--------------NGEPISSGSTRSRSLSGSNST---LTIS 62

                          90
                  ....*....|....
gi 167857792  112 RARRNDSGTYLCGA 125
Cdd:pfam13927  63 NVTRSDAGTYTCVA 76
IgV_TCR_beta cd05899
Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) beta chain; The members here ...
 38-130 4.09e-03

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: 36.11  E-value: 4.09e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792  38 SPALLVVTEGDNATFTCSFSNTSESFVlnWYRMSPSNQTDKLAAFPEDRSQPGQDC---RFRVTQlPNGRDFHMSVVRAR 114
Cdd:cd05899    4 SPRYLIKRRGQSVTLRCSQKSGHDNMY--WYRQDPGKGLQLLFYSYGGGLNEEGDLpgdRFSASR-PSLTRSSLTIKSAE 80

                         90
                 ....*....|....*.
gi 167857792 115 RNDSGTYLCgAISLAP 130
Cdd:cd05899   81 PEDSAVYLC-ASSLGG 95
I-set pfam07679
Immunoglobulin I-set domain;
42-125 5.57e-03

Immunoglobulin I-set domain;


Pssm-ID: 400151 [Multi-domain]  Cd Length: 90  Bit Score: 35.31  E-value: 5.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 167857792   42 LVVTEGDNATFTCSFSNTSEsFVLNWYRmspsnqtdklaafpeDRSQPGQDCRFRVTQlpNGRDFHMSVVRARRNDSGTY 121
Cdd:pfam07679  10 VEVQEGESARFTCTVTGTPD-PEVSWFK---------------DGQPLRSSDRFKVTY--EGGTYTLTISNVQPDDSGKY 71


                  ....
gi 167857792  122 LCGA 125
Cdd:pfam07679  72 TCVA 75
 
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