Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

P04234 (CD3D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 149. 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·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
T-cell surface glycoprotein CD3 delta chain
Alternative name(s):
T-cell receptor T3 delta chain
CD_antigen=CD3d
Gene names
Name:CD3D
Synonyms:T3D
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length171 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

The CD3 complex mediates signal transduction.

Subunit structure

The TCR/CD3 complex of T-lymphocytes consists of either a TCR alpha/beta or TCR gamma/delta heterodimer coexpressed at the cell surface with the invariant subunits of CD3 labeled gamma, delta, epsilon, zeta, and eta. Ref.12

Subcellular location

Membrane; Single-pass type I membrane protein.

Involvement in disease

Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (T(-)B(+)NK(+) SCID) [MIM:608971]: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.8

Sequence similarities

Contains 1 ITAM domain.

Ontologies

Keywords
   Cellular componentMembrane
   Coding sequence diversityAlternative splicing
Polymorphism
   DiseaseSCID
   DomainSignal
Transmembrane
Transmembrane helix
   Molecular functionReceptor
   PTMDisulfide bond
Glycoprotein
Phosphoprotein
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processT cell costimulation

Traceable author statement. Source: Reactome

T cell differentiation

Inferred from direct assay PubMed 2017177. Source: MGI

T cell receptor signaling pathway

Traceable author statement. Source: Reactome

cell surface receptor signaling pathway

Inferred by curator PubMed 9485181. Source: UniProtKB

positive regulation of transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 2017177. Source: MGI

positive thymic T cell selection

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of immune response

Traceable author statement. Source: Reactome

   Cellular_componentT cell receptor complex

Non-traceable author statement PubMed 9485181. Source: UniProtKB

alpha-beta T cell receptor complex

Inferred from electronic annotation. Source: Ensembl

cytoplasm

Non-traceable author statement PubMed 1831653. Source: UniProtKB

integral component of membrane

Inferred from electronic annotation. Source: UniProtKB-KW

plasma membrane

Traceable author statement. Source: Reactome

   Molecular_functionprotein heterodimerization activity

Inferred from physical interaction PubMed 9485181. Source: UniProtKB

transcription coactivator activity

Inferred from direct assay PubMed 2017177. Source: MGI

transmembrane signaling receptor activity

Inferred by curator PubMed 9485181. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P04234-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P04234-2)

The sequence of this isoform differs from the canonical sequence as follows:
     92-136: MCQSCVELDPATVAGIIVTDVIATLLLALGVFCFAGHETGRLSGA → T
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2121
Chain22 – 171150T-cell surface glycoprotein CD3 delta chain
PRO_0000016487

Regions

Topological domain22 – 10584Extracellular Potential
Transmembrane106 – 12621Helical; Potential
Topological domain127 – 17145Cytoplasmic Potential
Domain138 – 16629ITAM

Amino acid modifications

Modified residue1491Phosphotyrosine Ref.9 Ref.10
Modified residue1601Phosphotyrosine Ref.11
Glycosylation381N-linked (GlcNAc...) Potential
Glycosylation741N-linked (GlcNAc...) Potential
Disulfide bond37 ↔ 73 Ref.12

Natural variations

Alternative sequence92 – 13645MCQSC…RLSGA → T in isoform 2.
VSP_045800
Natural variant1471Q → R.
Corresponds to variant rs45510201 [ dbSNP | Ensembl ].
VAR_049646

Secondary structure

................. 171
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified March 20, 1987. Version 1.
Checksum: 6C1F248150186D21

FASTA17118,930
        10         20         30         40         50         60 
MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL 

        70         80         90        100        110        120 
GKRILDPRGI YRCNGTDIYK DKESTVQVHY RMCQSCVELD PATVAGIIVT DVIATLLLAL 

       130        140        150        160        170 
GVFCFAGHET GRLSGAADTQ ALLRNDQVYQ PLRDRDDAQY SHLGGNWARN K 

« Hide

Isoform 2 [UniParc].

Checksum: 1E879A1CC76B9856
Show »

FASTA12714,484

References

« Hide 'large scale' references
[1]"Exon/intron organization of the genes coding for the delta chains of the human and murine T-cell receptor/T3 complex."
van den Elsen P., Georgopoulos K., Shepley B.-A., Orkin S., Terhorst C.
Proc. Natl. Acad. Sci. U.S.A. 83:2944-2948(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Isolation of cDNA clones encoding the 20K T3 glycoprotein of human T-cell receptor complex."
van den Elsen P., Shepley B.-A., Borst J., Coligan J.E., Markham A.F., Orkin S., Terhorst C.
Nature 312:413-418(1984) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]"T3 delta pre-mRNA is transcribed from a non-TATA promoter and is alternatively spliced in human T cells."
Tunnacliffe A., Sims J.E., Rabbitts T.H.
EMBO J. 5:1245-1252(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]"PCR isolation and cloning of novel splice variant mRNAs from known drug target genes."
Jin P., Fu G.K., Wilson A.D., Yang J., Chien D., Hawkins P.R., Au-Young J., Stuve L.L.
Genomics 83:566-571(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
[5]"Human chromosome 11 DNA sequence and analysis including novel gene identification."
Taylor T.D., Noguchi H., Totoki Y., Toyoda A., Kuroki Y., Dewar K., Lloyd C., Itoh T., Takeda T., Kim D.-W., She X., Barlow K.F., Bloom T., Bruford E., Chang J.L., Cuomo C.A., Eichler E., FitzGerald M.G. expand/collapse author list , Jaffe D.B., LaButti K., Nicol R., Park H.-S., Seaman C., Sougnez C., Yang X., Zimmer A.R., Zody M.C., Birren B.W., Nusbaum C., Fujiyama A., Hattori M., Rogers J., Lander E.S., Sakaki Y.
Nature 440:497-500(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[6]"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] (ISOFORM 1).
Tissue: Blood.
[7]"Dephosphorylation of the human T lymphocyte CD3 antigen."
Alexander D., Goris J., Marais R., Rothbard J., Merlevede W., Crumpton M.J.
Eur. J. Biochem. 181:55-65(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: PROTEIN SEQUENCE OF 128-171.
[8]"Effect of CD3delta deficiency on maturation of alpha/beta and gamma/delta T-cell lineages in severe combined immunodeficiency."
Dadi H.K., Simon A.J., Roifman C.M.
N. Engl. J. Med. 349:1821-1828(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: INVOLVEMENT IN T(-)B(+)NK(+) SCID.
[9]"Profiling of tyrosine phosphorylation pathways in human cells using mass spectrometry."
Salomon A.R., Ficarro S.B., Brill L.M., Brinker A., Phung Q.T., Ericson C., Sauer K., Brock A., Horn D.M., Schultz P.G., Peters E.C.
Proc. Natl. Acad. Sci. U.S.A. 100:443-448(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Robust phosphoproteomic profiling of tyrosine phosphorylation sites from human T cells using immobilized metal affinity chromatography and tandem mass spectrometry."
Brill L.M., Salomon A.R., Ficarro S.B., Mukherji M., Stettler-Gill M., Peters E.C.
Anal. Chem. 76:2763-2772(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[11]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-160, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[12]"Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment."
Arnett K.L., Harrison S.C., Wiley D.C.
Proc. Natl. Acad. Sci. U.S.A. 101:16268-16273(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 23-100 IN COMPLEX WITH CD3E AND ANTIBODY FRAGMENT, SUBUNIT, DISULFIDE BOND.
+Additional computationally mapped references.

Web resources

CD3Dbase

CD3D mutation db

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X03934 Genomic DNA. Translation: CAA27573.1.
M12727, M12726 Genomic DNA. Translation: AAA51792.1.
CD014058 mRNA. No translation available.
AP001582 Genomic DNA. No translation available.
BC039035 mRNA. Translation: AAH39035.1.
BC070321 mRNA. Translation: AAH70321.1.
X01451 Genomic DNA. Translation: CAA25683.1.
PIRRWHUD1. A94706.
RefSeqNP_000723.1. NM_000732.4.
NP_001035741.1. NM_001040651.1.
UniGeneHs.504048.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1XIWX-ray1.90B/F23-100[»]
DisProtDP00505.
ProteinModelPortalP04234.
SMRP04234. Positions 23-95.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107353. 10 interactions.
IntActP04234. 3 interactions.
MINTMINT-3374023.
STRING9606.ENSP00000300692.

Chemistry

ChEMBLCHEMBL2364168.

PTM databases

PhosphoSiteP04234.

Polymorphism databases

DMDM115985.

Proteomic databases

PaxDbP04234.
PRIDEP04234.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000300692; ENSP00000300692; ENSG00000167286. [P04234-1]
ENST00000392884; ENSP00000376622; ENSG00000167286. [P04234-2]
GeneID915.
KEGGhsa:915.
UCSCuc001pss.1. human. [P04234-1]

Organism-specific databases

CTD915.
GeneCardsGC11M118212.
HGNCHGNC:1673. CD3D.
HPACAB013055.
MIM186790. gene.
608971. phenotype.
neXtProtNX_P04234.
Orphanet169160. T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta.
PharmGKBPA26215.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG41968.
HOGENOMHOG000015287.
HOVERGENHBG005278.
InParanoidP04234.
KOK06450.
OMAMCQSCVE.
OrthoDBEOG7S4X7Q.
PhylomeDBP04234.
TreeFamTF335892.

Enzyme and pathway databases

ReactomeREACT_6900. Immune System.

Gene expression databases

ArrayExpressP04234.
BgeeP04234.
CleanExHS_CD3D.
GenevestigatorP04234.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
InterProIPR015485. CD3_delta.
IPR015484. CD3_gsu/dsu.
IPR013783. Ig-like_fold.
IPR003110. Phos_immunorcpt_sig_ITAM.
[Graphical view]
PANTHERPTHR10570. PTHR10570. 1 hit.
PTHR10570:SF1. PTHR10570:SF1. 1 hit.
PfamPF02189. ITAM. 1 hit.
[Graphical view]
SMARTSM00077. ITAM. 1 hit.
[Graphical view]
PROSITEPS51055. ITAM_1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSCD3D. human.
EvolutionaryTraceP04234.
GeneWikiCD3D.
GenomeRNAi915.
NextBio3784.
PROP04234.
SOURCESearch...

Entry information

Entry nameCD3D_HUMAN
AccessionPrimary (citable) accession number: P04234
Secondary accession number(s): A8MVP6
Entry history
Integrated into UniProtKB/Swiss-Prot: March 20, 1987
Last sequence update: March 20, 1987
Last modified: April 16, 2014
This is version 149 of the entry and version 1 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 11

Human chromosome 11: entries, gene names and cross-references to MIM

Human cell differentiation molecules

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