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CD3D CD3d molecule [ Homo sapiens (human) ]

Gene ID: 915, updated on 20-Dec-2019

Summary

Official Symbol
CD3Dprovided by HGNC
Official Full Name
CD3d moleculeprovided by HGNC
Primary source
HGNC:HGNC:1673
See related
Ensembl:ENSG00000167286 MIM:186790
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; 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

Genomic context

See CD3D in Genome Data Viewer
Location:
11q23.3
Exon count:
5
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (118338954..118342744, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118209789..118213459, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 14251 Neighboring gene CD3e molecule Neighboring gene CD3g molecule Neighboring gene ubiquitination factor E4A Neighboring gene uncharacterized LOC100131626

Genomic regions, transcripts, and products

Expression

  • Project title: 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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein heterodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription coactivator activity IDA
Inferred from Direct Assay
more info
PubMed 
transmembrane signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
transmembrane signaling receptor activity IC
Inferred by Curator
more info
PubMed 
Process Evidence Code Pubs
T cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
T cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
T cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
cell surface receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell surface receptor signaling pathway IC
Inferred by Curator
more info
PubMed 
membrane organization TAS
Traceable Author Statement
more info
 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive thymic T cell selection IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive thymic T cell selection ISS
Inferred from Sequence or Structural Similarity
more info
 
protein homooligomerization IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of immune response TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
T cell receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
T cell receptor complex NAS
Non-traceable Author Statement
more info
PubMed 
alpha-beta T cell receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
clathrin-coated vesicle membrane TAS
Traceable Author Statement
more info
 
cytoplasm NAS
Non-traceable Author Statement
more info
PubMed 
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
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)

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_000732.4NP_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
    P04234
    UniProtKB/TrEMBL
    B0YIY4
    Related
    ENSP00000300692.4, ENST00000300692.8
    Conserved Domains (2) summary
    pfam02189
    Location:146165
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam16680
    Location:31100
    Ig_4; T-cell surface glycoprotein CD3 delta chain
  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, ENST00000392884.2
    Conserved Domains (2) summary
    pfam02189
    Location:102121
    ITAM; Immunoreceptor tyrosine-based activation motif
    cl11960
    Location:2591
    Ig; Immunoglobulin domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    118338954..118342744 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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