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Protein

Programmed cell death protein 1

Gene

PDCD1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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 - Biological processi

Keywordsi

Biological processApoptosis, 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

EuPathDBiHostDB:ENSG00000188389.10
HGNCiHGNC:8760 PDCD1
MIMi600244 gene
neXtProtiNX_Q15116

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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
Orphaneti802 NON RARE IN EUROPE: Multiple sclerosis
536 NON RARE IN EUROPE: Systemic lupus erythematosus
PharmGKBiPA33110

Chemistry databases

ChEMBLiCHEMBL3307223
DrugBankiDB05916 CT-011
DB09035 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...) asparagineSequence analysis1
Disulfide bondi54 ↔ 123PROSITE-ProRule annotation
Glycosylationi58N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi74N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi116N-linked (GlcNAc...) asparagineSequence analysis1

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ15116
PeptideAtlasiQ15116
PRIDEiQ15116
ProteomicsDBi60443

PTM databases

iPTMnetiQ15116
PhosphoSitePlusiQ15116

Expressioni

Developmental stagei

Induced at programmed cell death.

Gene expression databases

BgeeiENSG00000188389 Expressed in 78 organ(s), highest expression level in lymph node
CleanExiHS_PDCD1
ExpressionAtlasiQ15116 baseline and differential
GenevisibleiQ15116 HS

Organism-specific databases

HPAiCAB038418
CAB076386
HPA035981

Interactioni

Subunit structurei

Monomer.By similarity

Binary interactionsi

Protein-protein interaction databases

BioGridi111160, 61 interactors
DIPiDIP-44126N
IntActiQ15116, 7 interactors
MINTiQ15116
STRINGi9606.ENSP00000335062

Structurei

Secondary structure

1288
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ15116
SMRiQ15116
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

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

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

Gene3Di2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR013106 Ig_V-set
PfamiView protein in Pfam
PF07686 V-set, 1 hit
SMARTiView protein in SMART
SM00409 IG, 1 hit
SM00406 IGv, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit

Sequence (1+)i

Sequence statusi: Complete.

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

This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
H0Y2W6H0Y2W6_HUMAN
Programmed cell death protein 1
PDCD1
122Annotation score:
E7ER21E7ER21_HUMAN
Programmed cell death protein 1
PDCD1
66Annotation score:

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 dbSNP:rs2227982Ensembl.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

Similar proteinsi

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[»]
5B8CX-ray2.15C/F/I/L32-160[»]
5GGRX-ray3.30Y/Z26-150[»]
5GGSX-ray2.00Y/Z26-148[»]
5IUSX-ray2.89A/B26-146[»]
5JXEX-ray2.90A/B33-146[»]
5WT9X-ray2.40G1-167[»]
ProteinModelPortaliQ15116
SMRiQ15116
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi111160, 61 interactors
DIPiDIP-44126N
IntActiQ15116, 7 interactors
MINTiQ15116
STRINGi9606.ENSP00000335062

Chemistry databases

ChEMBLiCHEMBL3307223
DrugBankiDB05916 CT-011
DB09035 Nivolumab
DB09037 Pembrolizumab
GuidetoPHARMACOLOGYi2760

PTM databases

iPTMnetiQ15116
PhosphoSitePlusiQ15116

Polymorphism and mutation databases

BioMutaiPDCD1
DMDMi145559515

Proteomic databases

PaxDbiQ15116
PeptideAtlasiQ15116
PRIDEiQ15116
ProteomicsDBi60443

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
EuPathDBiHostDB:ENSG00000188389.10
GeneCardsiPDCD1
H-InvDBiHIX0030684
HGNCiHGNC:8760 PDCD1
HPAiCAB038418
CAB076386
HPA035981
MalaCardsiPDCD1
MIMi109100 phenotype
600244 gene
605218 phenotype
neXtProtiNX_Q15116
OpenTargetsiENSG00000188389
Orphaneti802 NON RARE IN EUROPE: Multiple sclerosis
536 NON RARE IN EUROPE: Systemic lupus erythematosus
PharmGKBiPA33110
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-389948 PD-1 signaling
SIGNORiQ15116

Miscellaneous databases

ChiTaRSiPDCD1 human
GeneWikiiProgrammed_cell_death_1
GenomeRNAii5133
PROiPR:Q15116
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000188389 Expressed in 78 organ(s), highest expression level in lymph node
CleanExiHS_PDCD1
ExpressionAtlasiQ15116 baseline and differential
GenevisibleiQ15116 HS

Family and domain databases

Gene3Di2.60.40.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003599 Ig_sub
IPR013106 Ig_V-set
PfamiView protein in Pfam
PF07686 V-set, 1 hit
SMARTiView protein in SMART
SM00409 IG, 1 hit
SM00406 IGv, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiPDCD1_HUMAN
AccessioniPrimary (citable) accession number: Q15116
Secondary accession number(s): O00517, Q8IX89
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: April 17, 2007
Last modified: November 7, 2018
This is version 166 of the entry and version 3 of the sequence. See 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 chromosome 2
    Human chromosome 2: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
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Main funding by: National Institutes of Health

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