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Q15116

- PDCD1_HUMAN

UniProt

Q15116 - PDCD1_HUMAN

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Protein

Programmed cell death protein 1

Gene
PDCD1, PD1
Organism
Homo sapiens (Human)
Status
Reviewed - 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

  1. protein binding Source: IntAct
  2. signal transducer activity Source: ProtInc

GO - Biological processi

  1. apoptotic process Source: ProtInc
  2. humoral immune response Source: ProtInc
  3. multicellular organismal development Source: ProtInc
  4. signal transduction Source: GOC
  5. T cell costimulation Source: Reactome
Complete GO annotation...

Keywords - Biological processi

Apoptosis, Immunity

Enzyme and pathway databases

ReactomeiREACT_19324. PD-1 signaling.

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
ProteomesiUP000005640: Chromosome 2

Organism-specific databases

HGNCiHGNC:8760. PDCD1.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini21 – 170150Extracellular Reviewed predictionAdd
BLAST
Transmembranei171 – 19121Helical; Reviewed predictionAdd
BLAST
Topological domaini192 – 28897Cytoplasmic Reviewed predictionAdd
BLAST

GO - Cellular componenti

  1. external side of plasma membrane Source: Ensembl
  2. integral component of membrane Source: UniProtKB-KW
  3. plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Membrane

Pathology & Biotechi

Involvement in diseasei

Systemic lupus erythematosus 2 (SLEB2) [MIM:605218]: A 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.
Note: Disease susceptibility is associated with variations affecting the gene represented in this entry.1 Publication

Keywords - Diseasei

Systemic lupus erythematosus

Organism-specific databases

MIMi109100. phenotype.
605218. phenotype.
Orphaneti802. Multiple sclerosis.
536. Systemic lupus erythematosus.
PharmGKBiPA33110.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2020 Reviewed predictionAdd
BLAST
Chaini21 – 288268Programmed cell death protein 1PRO_0000014892Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi49 – 491N-linked (GlcNAc...) Reviewed prediction
Disulfide bondi54 ↔ 123 By similarity
Glycosylationi58 – 581N-linked (GlcNAc...) Reviewed prediction
Glycosylationi74 – 741N-linked (GlcNAc...) Reviewed prediction
Glycosylationi116 – 1161N-linked (GlcNAc...) Reviewed prediction

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

PaxDbiQ15116.
PRIDEiQ15116.

PTM databases

PhosphoSiteiQ15116.

Expressioni

Developmental stagei

Induced at programmed cell death.

Gene expression databases

ArrayExpressiQ15116.
BgeeiQ15116.
CleanExiHS_PDCD1.
GenevestigatoriQ15116.

Organism-specific databases

HPAiHPA035981.

Interactioni

Subunit structurei

Monomer By similarity.

Binary interactionsi

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

Protein-protein interaction databases

BioGridi111160. 4 interactions.
IntActiQ15116. 4 interactions.
MINTiMINT-6488537.
STRINGi9606.ENSP00000335062.

Structurei

Secondary structure

1
288
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi36 – 383
Beta strandi40 – 456
Beta strandi50 – 556
Beta strandi63 – 7210
Beta strandi77 – 826
Beta strandi95 – 995
Beta strandi103 – 11210
Helixi115 – 1173
Beta strandi119 – 1279
Helixi129 – 1313
Beta strandi133 – 1364
Beta strandi140 – 1456

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2M2DNMR-A34-150[»]
3RRQX-ray2.10A32-160[»]
ProteinModelPortaliQ15116.
SMRiQ15116. Positions 34-150.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini35 – 145111Ig-like V-typeAdd
BLAST

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG46047.
HOGENOMiHOG000253959.
HOVERGENiHBG053534.
InParanoidiQ15116.
KOiK06744.
OMAiDFQWREK.
OrthoDBiEOG7966J2.
PhylomeDBiQ15116.
TreeFamiTF336181.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
InterProiIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013106. Ig_V-set.
IPR003596. Ig_V-set_subgr.
[Graphical view]
PfamiPF07686. V-set. 1 hit.
[Graphical view]
SMARTiSM00406. IGv. 1 hit.
[Graphical view]
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

MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA    50
TFTCSFSNTS ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL 100
PNGRDFHMSV VRARRNDSGT YLCGAISLAP KAQIKESLRA ELRVTERRAE 150
VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS LVLLVWVLAV ICSRAARGTI 200
GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP CVPEQTEYAT 250
IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL 288
Length:288
Mass (Da):31,647
Last modified:April 17, 2007 - v3
Checksum:iA5210FD40C304FB7
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti215 – 2151A → V.
Corresponds to variant rs2227982 [ dbSNP | Ensembl ].
VAR_031685

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti38 – 381S → F in AAC51773. 1 Publication
Sequence conflicti162 – 1621P → S in AAC41700. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
GeneIDi5133.
KEGGihsa:5133.
UCSCiuc002wcq.4. human.

Polymorphism databases

DMDMi145559515.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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 .
CCDSi CCDS33428.1.
PIRi A55737.
RefSeqi NP_005009.2. NM_005018.2.
UniGenei Hs.158297.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
2M2D NMR - A 34-150 [» ]
3RRQ X-ray 2.10 A 32-160 [» ]
ProteinModelPortali Q15116.
SMRi Q15116. Positions 34-150.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 111160. 4 interactions.
IntActi Q15116. 4 interactions.
MINTi MINT-6488537.
STRINGi 9606.ENSP00000335062.

Chemistry

GuidetoPHARMACOLOGYi 2760.

PTM databases

PhosphoSitei Q15116.

Polymorphism databases

DMDMi 145559515.

Proteomic databases

PaxDbi Q15116.
PRIDEi Q15116.

Protocols and materials databases

DNASUi 5133.
Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000334409 ; ENSP00000335062 ; ENSG00000188389 .
GeneIDi 5133.
KEGGi hsa:5133.
UCSCi uc002wcq.4. human.

Organism-specific databases

CTDi 5133.
GeneCardsi GC02M242792.
H-InvDB HIX0030684.
HGNCi HGNC:8760. PDCD1.
HPAi HPA035981.
MIMi 109100. phenotype.
600244. gene.
605218. phenotype.
neXtProti NX_Q15116.
Orphaneti 802. Multiple sclerosis.
536. Systemic lupus erythematosus.
PharmGKBi PA33110.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG46047.
HOGENOMi HOG000253959.
HOVERGENi HBG053534.
InParanoidi Q15116.
KOi K06744.
OMAi DFQWREK.
OrthoDBi EOG7966J2.
PhylomeDBi Q15116.
TreeFami TF336181.

Enzyme and pathway databases

Reactomei REACT_19324. PD-1 signaling.

Miscellaneous databases

GeneWikii Programmed_cell_death_1.
GenomeRNAii 5133.
NextBioi 19792.
PROi Q15116.
SOURCEi Search...

Gene expression databases

ArrayExpressi Q15116.
Bgeei Q15116.
CleanExi HS_PDCD1.
Genevestigatori Q15116.

Family and domain databases

Gene3Di 2.60.40.10. 1 hit.
InterProi IPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013106. Ig_V-set.
IPR003596. Ig_V-set_subgr.
[Graphical view ]
Pfami PF07686. V-set. 1 hit.
[Graphical view ]
SMARTi SM00406. IGv. 1 hit.
[Graphical view ]
PROSITEi PS50835. IG_LIKE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and chromosomal localization of the human PD-1 gene (PDCD1)."
    Shinohara T., Taniwaki M., Ishida Y., Kawaich M., Honjo T.
    Genomics 23:704-706(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The human PD-1 gene: complete cDNA, genomic organization, and developmentally regulated expression in B cell progenitors."
    Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., Burrows P.D., Billips L.D.
    Gene 197:177-187(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INVOLVEMENT IN SLEB2.
  4. "Cloning of PD-1 cDNA from activated peripheral leukocytes."
    He X., Xu L., Liu Y., Zeng Y.
    Submitted (FEB-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  5. Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  6. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  7. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  8. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  9. "The role of the PD-1 pathway in autoimmunity and peripheral tolerance."
    Fife B.T., Pauken K.E.
    Ann. N. Y. Acad. Sci. 1217:45-59(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

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: September 3, 2014
This is version 129 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

External Data

Dasty 3

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