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Q15116

- PDCD1_HUMAN

UniProt

Q15116 - PDCD1_HUMAN

Protein

Programmed cell death protein 1

Gene

PDCD1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 3 (17 Apr 2007)
      Previous versions | rss
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    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

    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

    GO - Cellular componenti

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

    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.1 Publication
    Note: Disease susceptibility is associated with variations affecting the gene represented in this entry.

    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 – 2020Sequence AnalysisAdd
    BLAST
    Chaini21 – 288268Programmed cell death protein 1PRO_0000014892Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Glycosylationi49 – 491N-linked (GlcNAc...)Sequence Analysis
    Disulfide bondi54 ↔ 123PROSITE-ProRule annotation
    Glycosylationi58 – 581N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi74 – 741N-linked (GlcNAc...)Sequence Analysis
    Glycosylationi116 – 1161N-linked (GlcNAc...)Sequence Analysis

    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.
    ModBaseiSearch...
    MobiDBiSearch...

    Topological domain

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Topological domaini21 – 170150ExtracellularSequence AnalysisAdd
    BLAST
    Topological domaini192 – 28897CytoplasmicSequence AnalysisAdd
    BLAST

    Transmembrane

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transmembranei171 – 19121HelicalSequence AnalysisAdd
    BLAST

    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

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti38 – 381S → F in AAC51773. (PubMed:9332365)Curated
    Sequence conflicti162 – 1621P → S in AAC41700. (PubMed:7851902)Curated

    Natural variant

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

    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

    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: October 1, 2014
    This is version 130 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