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    CD3D CD3 delta subunit of T-cell receptor complex [ Homo sapiens (human) ]

    Gene ID: 915, updated on 28-Oct-2024

    Summary

    Official Symbol
    CD3Dprovided by HGNC
    Official Full Name
    CD3 delta subunit of T-cell receptor complexprovided by HGNC
    Primary source
    HGNC:HGNC:1673
    See related
    Ensembl:ENSG00000167286 MIM:186790; AllianceGenome:HGNC:1673
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    T3D; IMD19; CD3DELTA; CD3-DELTA
    Summary
    The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined. [provided by RefSeq, Feb 2009]
    Expression
    Biased expression in lymph node (RPKM 30.2), appendix (RPKM 14.7) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CD3D in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118338954..118342705, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118355312..118360628, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118209669..118213420, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5587 Neighboring gene myelin protein zero like 2 Neighboring gene Sharpr-MPRA regulatory region 14251 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5588 Neighboring gene CD3 epsilon subunit of T-cell receptor complex Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5589 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:118220212-118221411 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5590 Neighboring gene CD3 gamma subunit of T-cell receptor complex Neighboring gene ubiquitination factor E4A Neighboring gene uncharacterized LOC100131626

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 inhibits CD3-induced Lck activation and cellular tyrosine phosphorylation, particularly of phosphoinositide-specific phospholipase C-gamma-1 PubMed
    env Binding of HIV-1 gp120 to the CD4 receptor molecule results in co-stimulation of CD3-induced T cell activation PubMed
    env HIV-1 envelope glycoproteins gp120 and gp160 directly and specifically impair the CD3/TcR-mediated activation of phospholipase C (PLC) via the CD4 molecule in uninfected T cells PubMed
    env HIV-1 gp120 induces CD4 association with lymphocyte surface molecules CD3, CD11a, CD27, CD45RA, CD45RB, CD45RO, CD49d, CD38, CD26, CD59, CD95 and class I MHC molecules PubMed
    env Treatment of CD4+ T cells with HIV-1 gp120 significantly increases CD4 association with CD3, CD45RA, CD45RB, CD59, CD38, CD26 and HLA class I, and decreases that with CD45RC PubMed
    Envelope surface glycoprotein gp160, precursor env HIV-1 gp160 interacts with CD3D; predicted interaction to be relevant to viral egress at plasma membrane/extracellular matrix PubMed
    Envelope transmembrane glycoprotein gp41 env Gp41 TMD co-localizes with the CD3-TCR complex and inhibits T-cell activation induced by antibodies to CD3 PubMed
    env HIV-1 gp41 peptide (amino acids 581-597) inhibits lymphoproliferation stimulated via the T-cell-activation molecules CD3, CD2, and CD28, as well as via direct stimulation mediated by phorbol ester combined with ionomycin PubMed
    Nef nef HIV-1 nef alleles from the great majority of primate lentiviruses, including HIV-2, downregulate TCR-CD3 from infected T cells and thereby block their responsiveness to activation PubMed
    nef HIV-1 Nef interacts with CD3 in living cells PubMed
    Pr55(Gag) gag Monocyte-derived macrophages selectively capture and engulf HIV-1-infected CD4+ T cells as HIV-1 Gag interacts with CD3 and Caspase 3 markers, leading to efficient macrophage infection PubMed
    gag CD3/28-treated resting CD4+ T cells produce more HIV-1 Gag protein than untreated cells PubMed
    gag Interferon-gamma can counteract the inhibitory effect of peptides based on the Capsid protein of HIV-1 Gag on antibody response to SRC PubMed
    gag Peptides corresponding to amino acids 218-238 of the Capsid protein of HIV-1 Gag inhibited anti-CD3-induced lymphoproliferation but did not directly affect anti-CD2 activation PubMed
    gag Synthetic peptides corresponding to amino acids 218-238 of the Capsid protein of HIV-1 Gag have been shown to inhibit in a dose dependent manner the induction of a specific antibody response to the sheep red cell (SRC) antigen through the T3-Ti complex PubMed
    Tat tat HIV-1 Tat interacts with CD3 and CD28 to co-stimulate IL-2 and IL-8 expression PubMed
    Vpu vpu HIV-1 Vpu interacts with CD3 in living cells PubMed
    capsid gag Synthetic peptides corresponding to amino acids 218-238 of HIV-1 Capsid have been shown to inhibit in a dose dependent manner the induction of a specific antibody response to the sheep red cell (SRC) antigen through the T3-Ti complex PubMed
    gag Interferon-gamma can counteract the inhibitory effect of HIV-1 Capsid based peptides on antibody response to SRC PubMed
    gag Peptides corresponding to amino acids 218-238 of HIV-1 Capsid inhibited anti-CD3-induced lymphoproliferation but did not directly affect anti-CD2 activation PubMed
    matrix gag HIV-1 MA co-localizes with CD3 marker protein in monocyte-derived macrophages cocultured with HIV-1-infected primary CD4+ T-cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transmembrane signaling receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transmembrane signaling receptor activity IC
    Inferred by Curator
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in T cell receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in adaptive immune response NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in alpha-beta T cell activation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in cell surface receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell surface receptor signaling pathway IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive thymic T cell selection IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive thymic T cell selection ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    part_of T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of alpha-beta T cell receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of alpha-beta T cell receptor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of alpha-beta T cell receptor complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of alpha-beta T cell receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in clathrin-coated endocytic vesicle membrane TAS
    Traceable Author Statement
    more info
     
    located_in cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    T-cell surface glycoprotein CD3 delta chain
    Names
    CD3 antigen, delta subunit
    CD3 delta
    CD3d antigen, delta polypeptide (TiT3 complex)
    CD3d molecule, delta (CD3-TCR complex)
    OKT3, delta chain
    T-cell receptor T3 delta chain

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_009891.1 RefSeqGene

      Range
      5001..8671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_37

    mRNA and Protein(s)

    1. NM_000732.6NP_000723.1  T-cell surface glycoprotein CD3 delta chain isoform A precursor

      See identical proteins and their annotated locations for NP_000723.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (A).
      Source sequence(s)
      BC070321
      Consensus CDS
      CCDS8394.1
      UniProtKB/Swiss-Prot
      A8MVP6, P04234
      UniProtKB/TrEMBL
      B0YIY4
      Related
      ENSP00000300692.4, ENST00000300692.9
      Conserved Domains (3) summary
      pfam02189
      Location:146165
      ITAM; Immunoreceptor tyrosine-based activation motif
      pfam16680
      Location:30104
      Ig_4; T-cell surface glycoprotein CD3 delta chain
      cd07691
      Location:3337
      IgC1_CD3_gamma_delta; Ig strand B [structural motif]
    2. NM_001040651.2NP_001035741.1  T-cell surface glycoprotein CD3 delta chain isoform B precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region, compared to variant 1. The encoded protein (B) is shorter and lacks the transmembrane domain, compared to isoform A.
      Source sequence(s)
      AP001582, BC070321, CD014058
      Consensus CDS
      CCDS41724.1
      UniProtKB/Swiss-Prot
      P04234
      Related
      ENSP00000376622.2, ENST00000392884.3
      Conserved Domains (2) summary
      pfam02189
      Location:102121
      ITAM; Immunoreceptor tyrosine-based activation motif
      cl11960
      Location:2591
      Ig; Immunoglobulin domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      118338954..118342705 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      118355312..118360628 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054370480.1XP_054226455.1  T-cell surface glycoprotein CD3 delta chain isoform X1

      UniProtKB/Swiss-Prot
      A8MVP6, P04234
      UniProtKB/TrEMBL
      B0YIY4