Reviewed, UniProtKB/Swiss-Prot P04234 (CD3D_HUMAN)

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	171 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence 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.11
Subcellular location	Membrane; Single-pass type I membrane protein.
Involvement in disease	Defects in CD3D are a cause of 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. Ref.6 Ref.7 Ref.8 Ref.9
Sequence similarities	Contains 1 ITAM domain.

Ontologies

Keywords
Cellular component	Membrane
Coding sequence diversity	Polymorphism
Disease	SCID
Domain	Signal Transmembrane
Molecular function	Receptor
PTM	Disulfide bond Glycoprotein Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	cell surface receptor linked signal transduction Inferred by curator. Source: UniProtKB positive thymic T cell selection Inferred from sequence or structural similarity. Source: UniProtKB
Cellular component	cytoplasm Non-traceable author statement. Source: UniProtKB integral to membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	protein heterodimerization activity Inferred from physical interaction. Source: UniProtKB transmembrane receptor activity Inferred by curator. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 21

21

Chain

22 – 171

150

T-cell surface glycoprotein CD3 delta chain

PRO_0000016487

Regions

Topological domain

22 – 105

84

Extracellular Potential

Transmembrane

106 – 126

21

Potential

Topological domain

127 – 171

45

Cytoplasmic Potential

Domain

138 – 166

29

ITAM

Amino acid modifications

Modified residue

149

1

Phosphotyrosine Ref.6 Ref.8 Ref.9

Modified residue

160

1

Phosphotyrosine Ref.6 Ref.8 Ref.9

Glycosylation

38

1

N-linked (GlcNAc...) Potential

Glycosylation

74

1

N-linked (GlcNAc...) Potential

Disulfide bond

37 ↔ 73

Ref.11

Natural variations

Natural variant

147

1

Q → R: dbSNP rs45510201.

VAR_049646

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

171

Helix Strand Turn

Details...

Beta strand

26 – 29

4

Beta strand

32 – 36

5

Beta strand

41 – 46

6

Beta strand

50 – 52

3

Helix

53 – 55

3

Beta strand

57 – 62

6

Helix

63 – 65

3

Beta strand

68 – 73

6

Beta strand

84 – 91

8

Sequences

	Sequence		Length	Mass (Da)
	P04234-1 [UniParc]. Last modified March 20, 1987. Version 1. Checksum: 6C1F248150186D21	FASTA	171	18,930
	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

References

	« Hide 'large scale' referencesShow '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: 2939461] [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: 6095101] [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: 3488209] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[4]	"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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Blood.
[5]	"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: 2540970] [Abstract] Cited for: PROTEIN SEQUENCE OF 128-171.
[6]	"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: 12522270] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149 AND TYR-160, MASS SPECTROMETRY.
[7]	"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: 14602880] [Abstract] Cited for: INVOLVEMENT IN T(-)/B(+)/NK(+) SCID.
[8]	"Immunoaffinity profiling of tyrosine phosphorylation in cancer cells." Rush J., Moritz A., Lee K.A., Guo A., Goss V.L., Spek E.J., Zhang H., Zha X.-M., Polakiewicz R.D., Comb M.J. Nat. Biotechnol. 23:94-101(2005) [PubMed: 15592455] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149 AND TYR-160, MASS SPECTROMETRY.
[9]	"Quantitative phosphoproteome analysis using a dendrimer conjugation chemistry and tandem mass spectrometry." Tao W.A., Wollscheid B., O'Brien R., Eng J.K., Li X.-J., Bodenmiller B., Watts J.D., Hood L., Aebersold R. Nat. Methods 2:591-598(2005) [PubMed: 16094384] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149 AND TYR-160, MASS SPECTROMETRY. Tissue: T-cell.
[10]	"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: 19690332] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149 AND TYR-160, MASS SPECTROMETRY. Tissue: T-cell.
[11]	"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: 15534202] [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

EMBLGenBankDDBJ

X03934 Genomic DNA. Translation: CAA27573.1.
M12727, M12726 Genomic DNA. Translation: AAA51792.1.
BC039035 mRNA. Translation: AAH39035.1.
BC070321 mRNA. Translation: AAH70321.1.
X01451 Genomic DNA. Translation: CAA25683.1.

IPI

IPI00022934.

PIR

RWHUD1. A94706.

RefSeq

NP_000723.1.
NP_001035741.1.

UniGene

Hs.2259
Hs.504048

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1XIW	X-ray	1.90	B/F	23-100	[»]

DisProt

DP00505.

ModBase

Search...

Protein-protein interaction databases

STRING

P04234.

PTM databases

PhosphoSite

P04234.

Proteomic databases

PRIDE

P04234.

Genome annotation databases

Ensembl

ENST00000300692; ENSP00000300692; ENSG00000167286; Homo sapiens. [Genome view]

GeneID

915.

KEGG

hsa:915.

UCSC

uc001pss.1. human.

Organism-specific databases

CTD

915.

GeneCards

GC11M117714.

H-InvDB

HIX0010180.

HGNC

HGNC:1673. CD3D.

HPA

CAB013055.

MIM

186790. gene.
608971. phenotype.

PharmGKB

PA26215.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

P04234.

HOVERGEN

P04234.

OMA

GHETGRL

OrthoDB

EOG99KJ9F

Enzyme and pathway databases

Pathway_Interaction_DB

cd8tcrdownstreampathway. Downstream signaling in naive CD8+ T cells.
il12_stat4pathway. IL12 signaling mediated by STAT4.
il12_2pathway. IL12-mediated signaling events.
tcrpathway. TCR signaling in naive CD4+ T cells.
cd8tcrpathway. TCR signaling in naive CD8+ T cells.

Reactome

REACT_6900. Signaling in Immune system.

Gene expression databases

ArrayExpress

P04234.

Bgee

P04234.

CleanEx

HS_CD3D.

Genevestigator

P04234.

GermOnline

ENSG00000167286. Homo sapiens.

Family and domain databases

InterPro

IPR015485. CD3_delta.
IPR015484. CD3_gsu/dsu.
IPR013783. Ig-like_fold.
IPR003110. Phos_immunorcpt_sig_ITAM.
[Graphical view]

Gene3D

G3DSA:2.60.40.10. Ig-like_fold. 1 hit.

PANTHER

PTHR10570:SF1. CD3_delta. 1 hit.
PTHR10570. CD3_gamma_delta. 1 hit.

Pfam

PF02189. ITAM. 1 hit.
[Graphical view]

SMART

SM00077. ITAM. 1 hit.
[Graphical view]

PROSITE

PS51055. ITAM_1. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

3784.

SOURCE

Search...

Entry information

Entry name

CD3D_HUMAN

Accession

Primary (citable) accession number: P04234

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 20, 1987
Last sequence update:	March 20, 1987
Last modified:	November 24, 2009
This is version 106 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

Disclaimer

Any 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.