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Protein

Programmed cell death protein 1

Gene

PDCD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Inhibitory cell surface receptor involved in the regulation of T-cell function during immunity and tolerance. Upon ligand binding, inhibits T-cell effector functions in an antigen-specific manner. Possible cell death inducer, in association with other factors.1 Publication

GO - Molecular functioni

  • signal transducer activity Source: ProtInc

GO - Biological processi

  • apoptotic process Source: ProtInc
  • humoral immune response Source: ProtInc
  • multicellular organism development Source: ProtInc
  • negative regulation of apoptotic process Source: Ensembl
  • negative regulation of tolerance induction Source: Ensembl
  • positive regulation of T cell apoptotic process Source: UniProtKB
  • T cell costimulation Source: Reactome
Complete GO annotation...

Keywords - Biological processi

Apoptosis, Immunity

Enzyme and pathway databases

ReactomeiR-HSA-389948. PD-1 signaling.
SIGNORiQ15116.

Names & Taxonomyi

Protein namesi
Recommended name:
Programmed cell death protein 1
Short name:
Protein PD-1
Short name:
hPD-1
Alternative name(s):
CD_antigen: CD279
Gene namesi
Name:PDCD1
Synonyms:PD1
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 2

Organism-specific databases

HGNCiHGNC:8760. PDCD1.

Subcellular locationi

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini21 – 170ExtracellularSequence analysisAdd BLAST150
Transmembranei171 – 191HelicalSequence analysisAdd BLAST21
Topological domaini192 – 288CytoplasmicSequence analysisAdd BLAST97

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Involvement in diseasei

Systemic lupus erythematosus 2 (SLEB2)1 Publication
Disease susceptibility is associated with variations affecting the gene represented in this entry.
Disease descriptionA chronic, relapsing, inflammatory, and often febrile multisystemic disorder of connective tissue, characterized principally by involvement of the skin, joints, kidneys and serosal membranes. It is of unknown etiology, but is thought to represent a failure of the regulatory mechanisms of the autoimmune system. The disease is marked by a wide range of system dysfunctions, an elevated erythrocyte sedimentation rate, and the formation of LE cells in the blood or bone marrow.
See also OMIM:605218

Keywords - Diseasei

Systemic lupus erythematosus

Organism-specific databases

DisGeNETi5133.
MalaCardsiPDCD1.
MIMi109100. phenotype.
605218. phenotype.
OpenTargetsiENSG00000188389.
ENSG00000276977.
Orphaneti802. Multiple sclerosis.
536. Systemic lupus erythematosus.
PharmGKBiPA33110.

Chemistry databases

ChEMBLiCHEMBL3307223.
DrugBankiDB09035. Nivolumab.
DB09037. Pembrolizumab.
GuidetoPHARMACOLOGYi2760.

Polymorphism and mutation databases

BioMutaiPDCD1.
DMDMi145559515.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 20Sequence analysisAdd BLAST20
ChainiPRO_000001489221 – 288Programmed cell death protein 1Add BLAST268

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi49N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi54 ↔ 123PROSITE-ProRule annotation
Glycosylationi58N-linked (GlcNAc...)Sequence analysis1
Glycosylationi74N-linked (GlcNAc...)Sequence analysis1
Glycosylationi116N-linked (GlcNAc...)Sequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ15116.
PeptideAtlasiQ15116.
PRIDEiQ15116.

PTM databases

iPTMnetiQ15116.
PhosphoSitePlusiQ15116.

Expressioni

Developmental stagei

Induced at programmed cell death.

Gene expression databases

BgeeiENSG00000188389.
CleanExiHS_PDCD1.
ExpressionAtlasiQ15116. baseline and differential.
GenevisibleiQ15116. HS.

Organism-specific databases

HPAiCAB038418.
HPA035981.

Interactioni

Subunit structurei

Monomer.By similarity

Binary interactionsi

WithEntry#Exp.IntActNotes
CD274Q9NZQ72EBI-4314328,EBI-4314282

Protein-protein interaction databases

BioGridi111160. 52 interactors.
DIPiDIP-44126N.
IntActiQ15116. 4 interactors.
MINTiMINT-6488537.
STRINGi9606.ENSP00000335062.

Structurei

Secondary structure

1288
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi36 – 38Combined sources3
Beta strandi40 – 45Combined sources6
Beta strandi50 – 55Combined sources6
Beta strandi63 – 72Combined sources10
Beta strandi77 – 82Combined sources6
Beta strandi95 – 99Combined sources5
Beta strandi103 – 112Combined sources10
Helixi115 – 117Combined sources3
Beta strandi119 – 127Combined sources9
Helixi129 – 131Combined sources3
Beta strandi133 – 136Combined sources4
Beta strandi140 – 145Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M2DNMR-A34-150[»]
3RRQX-ray2.10A32-160[»]
4ZQKX-ray2.45B33-150[»]
5IUSX-ray2.89A/B26-146[»]
5JXEX-ray2.90A/B33-146[»]
ProteinModelPortaliQ15116.
SMRiQ15116.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini35 – 145Ig-like V-typeAdd BLAST111

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410J26W. Eukaryota.
ENOG41116U6. LUCA.
GeneTreeiENSGT00390000013662.
HOGENOMiHOG000253959.
HOVERGENiHBG053534.
InParanoidiQ15116.
KOiK06744.
OMAiDFQWREK.
OrthoDBiEOG091G0EE8.
PhylomeDBiQ15116.
TreeFamiTF336181.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00406. IGv. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q15116-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA
60 70 80 90 100
TFTCSFSNTS ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL
110 120 130 140 150
PNGRDFHMSV VRARRNDSGT YLCGAISLAP KAQIKESLRA ELRVTERRAE
160 170 180 190 200
VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS LVLLVWVLAV ICSRAARGTI
210 220 230 240 250
GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP CVPEQTEYAT
260 270 280
IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL
Length:288
Mass (Da):31,647
Last modified:April 17, 2007 - v3
Checksum:iA5210FD40C304FB7
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti38S → F in AAC51773 (PubMed:9332365).Curated1
Sequence conflicti162P → S in AAC41700 (PubMed:7851902).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_031685215A → V.Corresponds to variant rs2227982dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27440 Genomic DNA. Translation: AAC41700.1.
U64863 mRNA. Translation: AAC51773.1.
AF363458 Genomic DNA. Translation: AAN64003.1.
AY238517 mRNA. Translation: AAO63583.1.
EF064716 Genomic DNA. Translation: ABK41899.1.
AK313848 mRNA. Translation: BAG36577.1.
CH471063 Genomic DNA. Translation: EAW71298.1.
BC074740 mRNA. Translation: AAH74740.1.
CCDSiCCDS33428.1.
PIRiA55737.
RefSeqiNP_005009.2. NM_005018.2.
UniGeneiHs.158297.

Genome annotation databases

EnsembliENST00000334409; ENSP00000335062; ENSG00000188389.
ENST00000618185; ENSP00000480684; ENSG00000276977.
GeneIDi5133.
KEGGihsa:5133.
UCSCiuc002wcq.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L27440 Genomic DNA. Translation: AAC41700.1.
U64863 mRNA. Translation: AAC51773.1.
AF363458 Genomic DNA. Translation: AAN64003.1.
AY238517 mRNA. Translation: AAO63583.1.
EF064716 Genomic DNA. Translation: ABK41899.1.
AK313848 mRNA. Translation: BAG36577.1.
CH471063 Genomic DNA. Translation: EAW71298.1.
BC074740 mRNA. Translation: AAH74740.1.
CCDSiCCDS33428.1.
PIRiA55737.
RefSeqiNP_005009.2. NM_005018.2.
UniGeneiHs.158297.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2M2DNMR-A34-150[»]
3RRQX-ray2.10A32-160[»]
4ZQKX-ray2.45B33-150[»]
5IUSX-ray2.89A/B26-146[»]
5JXEX-ray2.90A/B33-146[»]
ProteinModelPortaliQ15116.
SMRiQ15116.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111160. 52 interactors.
DIPiDIP-44126N.
IntActiQ15116. 4 interactors.
MINTiMINT-6488537.
STRINGi9606.ENSP00000335062.

Chemistry databases

ChEMBLiCHEMBL3307223.
DrugBankiDB09035. Nivolumab.
DB09037. Pembrolizumab.
GuidetoPHARMACOLOGYi2760.

PTM databases

iPTMnetiQ15116.
PhosphoSitePlusiQ15116.

Polymorphism and mutation databases

BioMutaiPDCD1.
DMDMi145559515.

Proteomic databases

PaxDbiQ15116.
PeptideAtlasiQ15116.
PRIDEiQ15116.

Protocols and materials databases

DNASUi5133.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000334409; ENSP00000335062; ENSG00000188389.
ENST00000618185; ENSP00000480684; ENSG00000276977.
GeneIDi5133.
KEGGihsa:5133.
UCSCiuc002wcq.5. human.

Organism-specific databases

CTDi5133.
DisGeNETi5133.
GeneCardsiPDCD1.
H-InvDBHIX0030684.
HGNCiHGNC:8760. PDCD1.
HPAiCAB038418.
HPA035981.
MalaCardsiPDCD1.
MIMi109100. phenotype.
600244. gene.
605218. phenotype.
neXtProtiNX_Q15116.
OpenTargetsiENSG00000188389.
ENSG00000276977.
Orphaneti802. Multiple sclerosis.
536. Systemic lupus erythematosus.
PharmGKBiPA33110.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410J26W. Eukaryota.
ENOG41116U6. LUCA.
GeneTreeiENSGT00390000013662.
HOGENOMiHOG000253959.
HOVERGENiHBG053534.
InParanoidiQ15116.
KOiK06744.
OMAiDFQWREK.
OrthoDBiEOG091G0EE8.
PhylomeDBiQ15116.
TreeFamiTF336181.

Enzyme and pathway databases

ReactomeiR-HSA-389948. PD-1 signaling.
SIGNORiQ15116.

Miscellaneous databases

GeneWikiiProgrammed_cell_death_1.
GenomeRNAii5133.
PROiQ15116.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000188389.
CleanExiHS_PDCD1.
ExpressionAtlasiQ15116. baseline and differential.
GenevisibleiQ15116. HS.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003599. Ig_sub.
IPR013106. Ig_V-set.
[Graphical view]
PfamiPF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00409. IG. 1 hit.
SM00406. IGv. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPDCD1_HUMAN
AccessioniPrimary (citable) accession number: Q15116
Secondary accession number(s): O00517, Q8IX89
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: April 17, 2007
Last modified: November 30, 2016
This is version 153 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.