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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.
27-SEP-2017, entry version 179.
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]
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).
[9]
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).
[10]
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).
[11]
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).
[12]
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).
[13]
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).
[14]
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: The CD3 complex mediates signal transduction.
-!- SUBUNIT: 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. {ECO:0000269|PubMed:15534202}.
-!- SUBCELLULAR LOCATION: 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.;
-!- 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; 5.
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: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; IPR007110; Ig-like_dom.
InterPro; IPR013783; Ig-like_fold.
InterPro; IPR032052; Ig_4.
InterPro; IPR003110; Phos_immunorcpt_sig_ITAM.
PANTHER; PTHR10570; PTHR10570; 1.
PANTHER; PTHR10570:SF11; PTHR10570:SF11; 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; Alternative splicing; Complete proteome;
Direct protein sequencing; Disulfide bond; Glycoprotein; 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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