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T-cell surface glycoprotein CD3 delta chain (T-cell receptor T3 delta chain) (CD antigen CD3d)

 CD3D_HUMAN              Reviewed;         171 AA.
P04234; A8MVP6;
20-MAR-1987, integrated into UniProtKB/Swiss-Prot.
20-MAR-1987, sequence version 1.
22-NOV-2017, entry version 181.
RecName: Full=T-cell surface glycoprotein CD3 delta chain;
AltName: Full=T-cell receptor T3 delta chain;
AltName: CD_antigen=CD3d;
Flags: Precursor;
Name=CD3D; Synonyms=T3D;
Homo sapiens (Human).
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
NCBI_TaxID=9606;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=2939461; DOI=10.1073/pnas.83.9.2944;
van den Elsen P., Georgopoulos K., Shepley B.-A., Orkin S.,
Terhorst C.;
"Exon/intron organization of the genes coding for the delta chains of
the human and murine T-cell receptor/T3 complex.";
Proc. Natl. Acad. Sci. U.S.A. 83:2944-2948(1986).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=6095101; DOI=10.1038/312413a0;
van den Elsen P., Shepley B.-A., Borst J., Coligan J.E., Markham A.F.,
Orkin S., Terhorst C.;
"Isolation of cDNA clones encoding the 20K T3 glycoprotein of human T-
cell receptor complex.";
Nature 312:413-418(1984).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=3488209;
Tunnacliffe A., Sims J.E., Rabbitts T.H.;
"T3 delta pre-mRNA is transcribed from a non-TATA promoter and is
alternatively spliced in human T cells.";
EMBO J. 5:1245-1252(1986).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
PubMed=15028279; DOI=10.1016/j.ygeno.2003.09.023;
Jin P., Fu G.K., Wilson A.D., Yang J., Chien D., Hawkins P.R.,
Au-Young J., Stuve L.L.;
"PCR isolation and cloning of novel splice variant mRNAs from known
drug target genes.";
Genomics 83:566-571(2004).
[5]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
PubMed=16554811; DOI=10.1038/nature04632;
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., 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.;
"Human chromosome 11 DNA sequence and analysis including novel gene
identification.";
Nature 440:497-500(2006).
[6]
NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
TISSUE=Blood;
PubMed=15489334; DOI=10.1101/gr.2596504;
The MGC Project Team;
"The status, quality, and expansion of the NIH full-length cDNA
project: the Mammalian Gene Collection (MGC).";
Genome Res. 14:2121-2127(2004).
[7]
PROTEIN SEQUENCE OF 128-171.
PubMed=2540970; DOI=10.1111/j.1432-1033.1989.tb14693.x;
Alexander D., Goris J., Marais R., Rothbard J., Merlevede W.,
Crumpton M.J.;
"Dephosphorylation of the human T lymphocyte CD3 antigen.";
Eur. J. Biochem. 181:55-65(1989).
[8]
FUNCTION, AND PHOSPHORYLATION BY LCK.
PubMed=2470098;
Barber E.K., Dasgupta J.D., Schlossman S.F., Trevillyan J.M.,
Rudd C.E.;
"The CD4 and CD8 antigens are coupled to a protein-tyrosine kinase
(p56lck) that phosphorylates the CD3 complex.";
Proc. Natl. Acad. Sci. U.S.A. 86:3277-3281(1989).
[9]
SUBUNIT.
PubMed=1828760;
Manolios N., Letourneur F., Bonifacino J.S., Klausner R.D.;
"Pairwise, cooperative and inhibitory interactions describe the
assembly and probable structure of the T-cell antigen receptor.";
EMBO J. 10:1643-1651(1991).
[10]
INTERACTION WITH CD4 AND CD8.
PubMed=1396954; DOI=10.1002/eji.1830221002;
Suzuki S., Kupsch J., Eichmann K., Saizawa M.K.;
"Biochemical evidence of the physical association of the majority of
CD3 delta chains with the accessory/co-receptor molecules CD4 and CD8
on nonactivated T lymphocytes.";
Eur. J. Immunol. 22:2475-2479(1992).
[11]
TISSUE SPECIFICITY.
PubMed=1372642;
Phillips J.H., Hori T., Nagler A., Bhat N., Spits H., Lanier L.L.;
"Ontogeny of human natural killer (NK) cells: fetal NK cells mediate
cytolytic function and express cytoplasmic CD3 epsilon,delta
proteins.";
J. Exp. Med. 175:1055-1066(1992).
[12]
FUNCTION, AND SUBUNIT.
PubMed=12507424;
Call M.E., Pyrdol J., Wiedmann M., Wucherpfennig K.W.;
"The organizing principle in the formation of the T cell receptor-CD3
complex.";
Cell 111:967-979(2002).
[13]
FUNCTION, AND INTERACTION WITH CD8.
PubMed=12215456; DOI=10.1074/jbc.M208119200;
Doucey M.A., Goffin L., Naeher D., Michielin O., Baumgaertner P.,
Guillaume P., Palmer E., Luescher I.F.;
"CD3 delta establishes a functional link between the T cell receptor
and CD8.";
J. Biol. Chem. 278:3257-3264(2003).
[14]
INVOLVEMENT IN IMD19.
PubMed=14602880; DOI=10.1056/NEJMoa031178;
Dadi H.K., Simon A.J., Roifman C.M.;
"Effect of CD3delta deficiency on maturation of alpha/beta and
gamma/delta T-cell lineages in severe combined immunodeficiency.";
N. Engl. J. Med. 349:1821-1828(2003).
[15]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=12522270; DOI=10.1073/pnas.2436191100;
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.;
"Profiling of tyrosine phosphorylation pathways in human cells using
mass spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 100:443-448(2003).
[16]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-149, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Leukemic T-cell;
PubMed=15144186; DOI=10.1021/ac035352d;
Brill L.M., Salomon A.R., Ficarro S.B., Mukherji M., Stettler-Gill M.,
Peters E.C.;
"Robust phosphoproteomic profiling of tyrosine phosphorylation sites
from human T cells using immobilized metal affinity chromatography and
tandem mass spectrometry.";
Anal. Chem. 76:2763-2772(2004).
[17]
INVOLVEMENT IN IMD19.
PubMed=15546002; DOI=10.1172/JCI22588;
de Saint Basile G., Geissmann F., Flori E., Uring-Lambert B.,
Soudais C., Cavazzana-Calvo M., Durandy A., Jabado N., Fischer A.,
Le Deist F.;
"Severe combined immunodeficiency caused by deficiency in either the
delta or the epsilon subunit of CD3.";
J. Clin. Invest. 114:1512-1517(2004).
[18]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-160, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
TISSUE=Leukemic T-cell;
PubMed=19690332; DOI=10.1126/scisignal.2000007;
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K.,
Rodionov V., Han D.K.;
"Quantitative phosphoproteomic analysis of T cell receptor signaling
reveals system-wide modulation of protein-protein interactions.";
Sci. Signal. 2:RA46-RA46(2009).
[19]
INVOLVEMENT IN IMD19.
PubMed=21883749; DOI=10.1111/j.1399-3046.2011.01563.x;
Yu G.P., Nadeau K.C., Berk D.R., de Saint Basile G., Lambert N.,
Knapnougel P., Roberts J., Kavanau K., Dunn E., Stiehm E.R.,
Lewis D.B., Umetsu D.T., Puck J.M., Cowan M.J.;
"Genotype, phenotype, and outcomes of nine patients with T-B+NK+
SCID.";
Pediatr. Transplant. 15:733-741(2011).
[20]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 23-100 IN COMPLEX WITH CD3E
AND ANTIBODY FRAGMENT, SUBUNIT, AND DISULFIDE BOND.
PubMed=15534202; DOI=10.1073/pnas.0407359101;
Arnett K.L., Harrison S.C., Wiley D.C.;
"Crystal structure of a human CD3-epsilon/delta dimer in complex with
a UCHT1 single-chain antibody fragment.";
Proc. Natl. Acad. Sci. U.S.A. 101:16268-16273(2004).
-!- FUNCTION: Part of the TCR-CD3 complex present on T-lymphocyte cell
surface that plays an essential role in adaptive immune response.
When antigen presenting cells (APCs) activate T-cell receptor
(TCR), TCR-mediated signals are transmitted across the cell
membrane by the CD3 chains CD3D, CD3E, CD3G and CD3Z. All CD3
chains contain immunoreceptor tyrosine-based activation motifs
(ITAMs) in their cytoplasmic domain. Upon TCR engagement, these
motifs become phosphorylated by Src family protein tyrosine
kinases LCK and FYN, resulting in the activation of downstream
signaling pathways (PubMed:2470098). In addition of this role of
signal transduction in T-cell activation, CD3D plays an essential
role in thymocyte differentiation. Indeed, participates in correct
intracellular TCR-CD3 complex assembly and surface expression. In
absence of a functional TCR-CD3 complex, thymocytes are unable to
differentiate properly. Interacts with CD4 and CD8 and thus serves
to establish a functional link between the TCR and coreceptors CD4
and CD8, which is needed for activation and positive selection of
CD4 or CD8 T-cells(PubMed:12215456). {ECO:0000269|PubMed:12215456,
ECO:0000269|PubMed:12507424, ECO:0000269|PubMed:2470098}.
-!- SUBUNIT: The TCR-CD3 complex is composed of a CD3D/CD3E and a
CD3G/CD3E heterodimers that preferentially associate with TCRalpha
and TCRbeta, respectively, to form TCRalpha/CD3E/CD3G and
TCRbeta/CD3G/CD3E trimers. In turn, the hexamer interacts with
CD3Z homodimer to form the TCR-CD3 complex. Alternatively,
TCRalpha and TCRbeta can be replaced by TCRgamma and TCRdelta.
Interacts with coreceptors CD4 and CD8 (PubMed:1396954,
PubMed:12215456). {ECO:0000269|PubMed:12215456,
ECO:0000269|PubMed:12507424, ECO:0000269|PubMed:1396954,
ECO:0000269|PubMed:15534202, ECO:0000269|PubMed:1828760}.
-!- SUBCELLULAR LOCATION: Cell membrane; Single-pass type I membrane
protein.
-!- ALTERNATIVE PRODUCTS:
Event=Alternative splicing; Named isoforms=2;
Name=1;
IsoId=P04234-1; Sequence=Displayed;
Name=2;
IsoId=P04234-2; Sequence=VSP_045800;
Note=No experimental confirmation available.;
-!- TISSUE SPECIFICITY: CD3D is mostly present on T-lymphocytes with
its TCR-CD3 partners. Present also in fetal NK-cells.
{ECO:0000269|PubMed:1372642}.
-!- PTM: Phosphorylated on Tyr residues after T-cell receptor
triggering by LCK in association with CD4/CD8.
{ECO:0000269|PubMed:2470098}.
-!- DISEASE: Immunodeficiency 19 (IMD19) [MIM:615617]: An autosomal
recessive form of severe combined immunodeficiency characterized
by onset in early infancy of recurrent bacterial, viral, and
fungal infections. Patients usually have chronic diarrhea,
recurrent respiratory infections, and failure to thrive.
Immunologic work-up shows a T-cell negative, B-cell positive, NK-
cell positive phenotype. {ECO:0000269|PubMed:14602880,
ECO:0000269|PubMed:15546002, ECO:0000269|PubMed:21883749}.
Note=The disease is caused by mutations affecting the gene
represented in this entry.
-!- WEB RESOURCE: Name=CD3Dbase; Note=CD3D mutation db;
URL="http://structure.bmc.lu.se/idbase/CD3Dbase/";
-----------------------------------------------------------------------
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EMBL; X03934; CAA27573.1; -; Genomic_DNA.
EMBL; M12727; AAA51792.1; -; Genomic_DNA.
EMBL; M12726; AAA51792.1; JOINED; Genomic_DNA.
EMBL; CD014058; -; NOT_ANNOTATED_CDS; mRNA.
EMBL; AP001582; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; BC039035; AAH39035.1; -; mRNA.
EMBL; BC070321; AAH70321.1; -; mRNA.
EMBL; X01451; CAA25683.1; -; Genomic_DNA.
CCDS; CCDS41724.1; -. [P04234-2]
CCDS; CCDS8394.1; -. [P04234-1]
PIR; A94706; RWHUD1.
RefSeq; NP_000723.1; NM_000732.4. [P04234-1]
RefSeq; NP_001035741.1; NM_001040651.1. [P04234-2]
RefSeq; XP_016874032.1; XM_017018543.1. [P04234-1]
UniGene; Hs.504048; -.
PDB; 1XIW; X-ray; 1.90 A; B/F=23-100.
PDBsum; 1XIW; -.
DisProt; DP00505; -.
ProteinModelPortal; P04234; -.
SMR; P04234; -.
BioGrid; 107353; 9.
DIP; DIP-42855N; -.
ELM; P04234; -.
IntAct; P04234; 6.
MINT; MINT-3374023; -.
STRING; 9606.ENSP00000300692; -.
ChEMBL; CHEMBL2364168; -.
DrugBank; DB09052; Blinatumomab.
DrugBank; DB00075; Muromonab.
iPTMnet; P04234; -.
PhosphoSitePlus; P04234; -.
SwissPalm; P04234; -.
BioMuta; CD3D; -.
DMDM; 115985; -.
MaxQB; P04234; -.
PaxDb; P04234; -.
PeptideAtlas; P04234; -.
PRIDE; P04234; -.
Ensembl; ENST00000300692; ENSP00000300692; ENSG00000167286. [P04234-1]
Ensembl; ENST00000392884; ENSP00000376622; ENSG00000167286. [P04234-2]
GeneID; 915; -.
KEGG; hsa:915; -.
UCSC; uc001pss.2; human. [P04234-1]
CTD; 915; -.
DisGeNET; 915; -.
EuPathDB; HostDB:ENSG00000167286.9; -.
GeneCards; CD3D; -.
HGNC; HGNC:1673; CD3D.
HPA; CAB013055; -.
MalaCards; CD3D; -.
MIM; 186790; gene.
MIM; 615617; phenotype.
neXtProt; NX_P04234; -.
OpenTargets; ENSG00000167286; -.
Orphanet; 169160; T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta.
PharmGKB; PA26215; -.
eggNOG; ENOG410IWAX; Eukaryota.
eggNOG; ENOG410Y2TD; LUCA.
GeneTree; ENSGT00510000046930; -.
HOGENOM; HOG000015287; -.
HOVERGEN; HBG005278; -.
InParanoid; P04234; -.
KO; K06450; -.
OMA; MCQSCVE; -.
OrthoDB; EOG091G0U7X; -.
PhylomeDB; P04234; -.
TreeFam; TF335892; -.
Reactome; R-HSA-198933; Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.
Reactome; R-HSA-202424; Downstream TCR signaling.
Reactome; R-HSA-202427; Phosphorylation of CD3 and TCR zeta chains.
Reactome; R-HSA-202430; Translocation of ZAP-70 to Immunological synapse.
Reactome; R-HSA-202433; Generation of second messenger molecules.
Reactome; R-HSA-389948; PD-1 signaling.
Reactome; R-HSA-8856825; Cargo recognition for clathrin-mediated endocytosis.
Reactome; R-HSA-8856828; Clathrin-mediated endocytosis.
ChiTaRS; CD3D; human.
EvolutionaryTrace; P04234; -.
GeneWiki; CD3D; -.
GenomeRNAi; 915; -.
PRO; PR:P04234; -.
Proteomes; UP000005640; Chromosome 11.
Bgee; ENSG00000167286; -.
CleanEx; HS_CD3D; -.
ExpressionAtlas; P04234; baseline and differential.
Genevisible; P04234; HS.
GO; GO:0042105; C:alpha-beta T cell receptor complex; IEA:Ensembl.
GO; GO:0030665; C:clathrin-coated vesicle membrane; TAS:Reactome.
GO; GO:0005737; C:cytoplasm; NAS:UniProtKB.
GO; GO:0016021; C:integral component of membrane; IEA:UniProtKB-KW.
GO; GO:0005886; C:plasma membrane; TAS:Reactome.
GO; GO:0042101; C:T cell receptor complex; IDA:MGI.
GO; GO:0046982; F:protein heterodimerization activity; IPI:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IMP:CAFA.
GO; GO:0003713; F:transcription coactivator activity; IDA:MGI.
GO; GO:0004888; F:transmembrane signaling receptor activity; IC:UniProtKB.
GO; GO:0002250; P:adaptive immune response; IEA:UniProtKB-KW.
GO; GO:0007166; P:cell surface receptor signaling pathway; IC:UniProtKB.
GO; GO:0061024; P:membrane organization; TAS:Reactome.
GO; GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:MGI.
GO; GO:0045059; P:positive thymic T cell selection; ISS:UniProtKB.
GO; GO:0051260; P:protein homooligomerization; IMP:CAFA.
GO; GO:0050776; P:regulation of immune response; TAS:Reactome.
GO; GO:0031295; P:T cell costimulation; TAS:Reactome.
GO; GO:0030217; P:T cell differentiation; IDA:MGI.
GO; GO:0050852; P:T cell receptor signaling pathway; TAS:Reactome.
Gene3D; 2.60.40.10; -; 1.
InterPro; IPR015484; CD3_esu/gsu/dsu.
InterPro; IPR015485; CD3D.
InterPro; IPR036179; Ig-like_dom_sf.
InterPro; IPR013783; Ig-like_fold.
InterPro; IPR032052; Ig_4.
InterPro; IPR003110; Phos_immunorcpt_sig_ITAM.
PANTHER; PTHR10570; PTHR10570; 1.
PANTHER; PTHR10570:SF5; PTHR10570:SF5; 1.
Pfam; PF16680; Ig_4; 1.
Pfam; PF02189; ITAM; 1.
SMART; SM00077; ITAM; 1.
SUPFAM; SSF48726; SSF48726; 1.
PROSITE; PS51055; ITAM_1; 1.
1: Evidence at protein level;
3D-structure; Adaptive immunity; Alternative splicing; Cell membrane;
Complete proteome; Direct protein sequencing; Disulfide bond;
Glycoprotein; Immunity; Membrane; Phosphoprotein; Polymorphism;
Receptor; Reference proteome; SCID; Signal; Transmembrane;
Transmembrane helix.
SIGNAL 1 21
CHAIN 22 171 T-cell surface glycoprotein CD3 delta
chain.
/FTId=PRO_0000016487.
TOPO_DOM 22 105 Extracellular. {ECO:0000255}.
TRANSMEM 106 126 Helical. {ECO:0000255}.
TOPO_DOM 127 171 Cytoplasmic. {ECO:0000255}.
DOMAIN 138 166 ITAM. {ECO:0000255|PROSITE-
ProRule:PRU00379}.
MOD_RES 149 149 Phosphotyrosine.
{ECO:0000244|PubMed:12522270,
ECO:0000244|PubMed:15144186}.
MOD_RES 160 160 Phosphotyrosine.
{ECO:0000244|PubMed:19690332}.
CARBOHYD 38 38 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
CARBOHYD 74 74 N-linked (GlcNAc...) asparagine.
{ECO:0000255}.
DISULFID 37 73 {ECO:0000269|PubMed:15534202}.
VAR_SEQ 92 136 MCQSCVELDPATVAGIIVTDVIATLLLALGVFCFAGHETGR
LSGA -> T (in isoform 2).
{ECO:0000303|PubMed:15028279}.
/FTId=VSP_045800.
VARIANT 147 147 Q -> R (in dbSNP:rs45510201).
/FTId=VAR_049646.
STRAND 26 29 {ECO:0000244|PDB:1XIW}.
STRAND 32 36 {ECO:0000244|PDB:1XIW}.
STRAND 41 46 {ECO:0000244|PDB:1XIW}.
STRAND 50 52 {ECO:0000244|PDB:1XIW}.
HELIX 53 55 {ECO:0000244|PDB:1XIW}.
STRAND 57 62 {ECO:0000244|PDB:1XIW}.
HELIX 63 65 {ECO:0000244|PDB:1XIW}.
STRAND 68 73 {ECO:0000244|PDB:1XIW}.
STRAND 84 91 {ECO:0000244|PDB:1XIW}.
SEQUENCE 171 AA; 18930 MW; 6C1F248150186D21 CRC64;
MEHSTFLSGL VLATLLSQVS PFKIPIEELE DRVFVNCNTS ITWVEGTVGT LLSDITRLDL
GKRILDPRGI YRCNGTDIYK DKESTVQVHY RMCQSCVELD PATVAGIIVT DVIATLLLAL
GVFCFAGHET GRLSGAADTQ ALLRNDQVYQ PLRDRDDAQY SHLGGNWARN K


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