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Q15116 (PDCD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 128. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (7) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Programmed cell death protein 1

Short name=Protein PD-1
Short name=hPD-1
Alternative name(s):
CD_antigen=CD279
Gene names
Name:PDCD1
Synonyms:PD1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length288 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.10

Subunit structure

Monomer By similarity.

Subcellular location

Membrane; Single-pass type I membrane protein.

Developmental stage

Induced at programmed cell death.

Involvement in disease

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. Ref.4

Sequence similarities

Contains 1 Ig-like V-type (immunoglobulin-like) domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

CD274Q9NZQ72EBI-4314328,EBI-4314282

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2020 Potential
Chain21 – 288268Programmed cell death protein 1
PRO_0000014892

Regions

Topological domain21 – 170150Extracellular Potential
Transmembrane171 – 19121Helical; Potential
Topological domain192 – 28897Cytoplasmic Potential
Domain35 – 145111Ig-like V-type

Amino acid modifications

Glycosylation491N-linked (GlcNAc...) Potential
Glycosylation581N-linked (GlcNAc...) Potential
Glycosylation741N-linked (GlcNAc...) Potential
Glycosylation1161N-linked (GlcNAc...) Potential
Disulfide bond54 ↔ 123 By similarity

Natural variations

Natural variant2151A → V.
Corresponds to variant rs2227982 [ dbSNP | Ensembl ].
VAR_031685

Experimental info

Sequence conflict381S → F in AAC51773. Ref.2
Sequence conflict1621P → S in AAC41700. Ref.1

Secondary structure

......................... 288
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q15116 [UniParc].

Last modified April 17, 2007. Version 3.
Checksum: A5210FD40C304FB7

FASTA28831,647
        10         20         30         40         50         60 
MQIPQAPWPV VWAVLQLGWR PGWFLDSPDR PWNPPTFSPA LLVVTEGDNA TFTCSFSNTS 

        70         80         90        100        110        120 
ESFVLNWYRM SPSNQTDKLA AFPEDRSQPG QDCRFRVTQL PNGRDFHMSV VRARRNDSGT 

       130        140        150        160        170        180 
YLCGAISLAP KAQIKESLRA ELRVTERRAE VPTAHPSPSP RPAGQFQTLV VGVVGGLLGS 

       190        200        210        220        230        240 
LVLLVWVLAV ICSRAARGTI GARRTGQPLK EDPSAVPVFS VDYGELDFQW REKTPEPPVP 

       250        260        270        280 
CVPEQTEYAT IVFPSGMGTS SPARRGSADG PRSAQPLRPE DGHCSWPL 

« Hide

References

« Hide 'large scale' references
[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]Erratum
Finger L.R., Pu J., Wasserman R., Vibhakar R., Louie E., Hardy R.R., Burrows P.D., Billips L.D.
Gene 203:253-253(1997)
[4]"A regulatory polymorphism in PDCD1 is associated with susceptibility to systemic lupus erythematosus in humans."
Prokunina L., Castillejo-Lopez C., Oberg F., Gunnarsson I., Berg L., Magnusson V., Brookes A.J., Tentler D., Kristjansdottir H., Grondal G., Bolstad A.I., Svenungsson E., Lundberg I., Sturfelt G., Jonssen A., Truedsson L., Lima G., Alcocer-Varela J. expand/collapse author list , Jonsson R., Gyllensten U.B., Harley J.B., Alarcon-Segovia D., Steinsson K., Alarcon-Riquelme M.E.
Nat. Genet. 32:666-669(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], INVOLVEMENT IN SLEB2.
[5]"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].
[6]Livingston R.J., Shaffer T., McFarland I., Nguyen C.P., Stanaway I.B., Rajkumar N., Johnson E.J., da Ponte S.H., Willa H., Ahearn M.O., Bertucci C., Acklestad J., Carroll A., Swanson J., Gildersleeve H.I., Nickerson D.A.
Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[7]"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. expand/collapse author list , 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].
[8]"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].
[9]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[10]"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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
CCDSCCDS33428.1.
PIRA55737.
RefSeqNP_005009.2. NM_005018.2.
UniGeneHs.158297.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2M2DNMR-A34-150[»]
3RRQX-ray2.10A32-160[»]
ProteinModelPortalQ15116.
SMRQ15116. Positions 34-150.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid111160. 4 interactions.
IntActQ15116. 4 interactions.
MINTMINT-6488537.
STRING9606.ENSP00000335062.

Chemistry

GuidetoPHARMACOLOGY2760.

PTM databases

PhosphoSiteQ15116.

Polymorphism databases

DMDM145559515.

Proteomic databases

PaxDbQ15116.
PRIDEQ15116.

Protocols and materials databases

DNASU5133.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000334409; ENSP00000335062; ENSG00000188389.
GeneID5133.
KEGGhsa:5133.
UCSCuc002wcq.4. human.

Organism-specific databases

CTD5133.
GeneCardsGC02M242792.
H-InvDBHIX0030684.
HGNCHGNC:8760. PDCD1.
HPAHPA035981.
MIM109100. phenotype.
600244. gene.
605218. phenotype.
neXtProtNX_Q15116.
Orphanet802. Multiple sclerosis.
536. Systemic lupus erythematosus.
PharmGKBPA33110.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG46047.
HOGENOMHOG000253959.
HOVERGENHBG053534.
InParanoidQ15116.
KOK06744.
OMADFQWREK.
OrthoDBEOG7966J2.
PhylomeDBQ15116.
TreeFamTF336181.

Enzyme and pathway databases

ReactomeREACT_6900. Immune System.

Gene expression databases

ArrayExpressQ15116.
BgeeQ15116.
CleanExHS_PDCD1.
GenevestigatorQ15116.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR013106. Ig_V-set.
IPR003596. Ig_V-set_subgr.
[Graphical view]
PfamPF07686. V-set. 1 hit.
[Graphical view]
SMARTSM00406. IGv. 1 hit.
[Graphical view]
PROSITEPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiProgrammed_cell_death_1.
GenomeRNAi5133.
NextBio19792.
PROQ15116.
SOURCESearch...

Entry information

Entry namePDCD1_HUMAN
AccessionPrimary (citable) accession number: Q15116
Secondary accession number(s): O00517, Q8IX89
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: April 17, 2007
Last modified: July 9, 2014
This is version 128 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 2

Human chromosome 2: entries, gene names and cross-references to MIM

Human cell differentiation molecules

CD nomenclature of surface proteins of human leucocytes and list of entries