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P15813 (CD1D_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 145. 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·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Antigen-presenting glycoprotein CD1d
Alternative name(s):
R3G1
CD_antigen=CD1d
Gene names
Name:CD1D
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length335 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. Ref.11

Subunit structure

Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II. Ref.9

Subcellular location

Cell membrane; Single-pass type I membrane protein. Endosome membrane. Lysosome membrane. Note: Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes. Ref.8 Ref.9 Ref.11

Tissue specificity

Expressed on cortical thymocytes, on certain T-cell leukemias, and in various other tissues.

Miscellaneous

During protein synthesis and maturation, CD1 family members bind endogenous lipids that are replaced by lipid or glycolipid antigens when the proteins are internalized and pass through endosomes, before trafficking back to the cell surface By similarity.

Sequence similarities

Contains 1 Ig-like (immunoglobulin-like) domain.

Ontologies

Keywords
   Biological processHost-virus interaction
Immunity
Innate immunity
   Cellular componentCell membrane
Endosome
Lysosome
Membrane
   Coding sequence diversityPolymorphism
   DomainImmunoglobulin domain
Signal
Transmembrane
Transmembrane helix
   PTMDisulfide bond
Glycoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processT cell selection

Traceable author statement PubMed 14500461. Source: UniProtKB

antigen processing and presentation, endogenous lipid antigen via MHC class Ib

Inferred from direct assay PubMed 10523605. Source: UniProtKB

antigen processing and presentation, exogenous lipid antigen via MHC class Ib

Inferred from Biological aspect of Ancestor. Source: RefGenome

detection of bacterium

Traceable author statement PubMed 14500461. Source: UniProtKB

heterotypic cell-cell adhesion

Traceable author statement PubMed 19124746. Source: BHF-UCL

innate immune response

Inferred from electronic annotation. Source: UniProtKB-KW

positive regulation of T cell proliferation

Inferred from direct assay PubMed 19124746. Source: BHF-UCL

positive regulation of innate immune response

Traceable author statement PubMed 14500461. Source: UniProtKB

viral process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentcell surface

Inferred from direct assay PubMed 19124746. Source: BHF-UCL

cytoplasm

Inferred from direct assay PubMed 19124746. Source: BHF-UCL

endosome membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

integral component of plasma membrane

Traceable author statement PubMed 11315191. Source: UniProtKB

lysosomal membrane

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionbeta-2-microglobulin binding

Traceable author statement PubMed 14500461. Source: UniProtKB

cell adhesion molecule binding

Inferred from physical interaction PubMed 19124746. Source: BHF-UCL

endogenous lipid antigen binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

exogenous lipid antigen binding

Inferred from direct assay PubMed 10523605. Source: UniProtKB

histone binding

Inferred from physical interaction PubMed 20363964. Source: UniProtKB

lipid antigen binding

Inferred from direct assay PubMed 19124746. Source: BHF-UCL

lipopeptide binding

Inferred from Biological aspect of Ancestor. Source: RefGenome

receptor activity

Inferred by curator PubMed 11315191. Source: UniProtKB

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1919 Potential
Chain20 – 335316Antigen-presenting glycoprotein CD1d
PRO_0000014581

Regions

Topological domain20 – 301282Extracellular Potential
Transmembrane302 – 32221Helical; Potential
Topological domain323 – 33513Cytoplasmic Potential
Domain185 – 292108Ig-like
Motif331 – 3344Internalization signal

Sites

Binding site981Glycolipid
Binding site1691Glycolipid
Binding site1721Glycolipid

Amino acid modifications

Glycosylation381N-linked (GlcNAc...) Ref.14
Glycosylation601N-linked (GlcNAc...) Ref.12 Ref.14
Glycosylation1261N-linked (GlcNAc...) Potential
Glycosylation1811N-linked (GlcNAc...) Potential
Disulfide bond120 ↔ 184 Ref.13
Disulfide bond224 ↔ 279 Ref.13

Natural variations

Natural variant641T → S. Ref.6
Corresponds to variant rs62621276 [ dbSNP | Ensembl ].
VAR_010211

Experimental info

Mutagenesis3311Y → A: Strongly reduced internalization. Ref.8
Mutagenesis3341V → A: Strongly reduced internalization. Ref.8

Secondary structure

.................................................. 335
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P15813 [UniParc].

Last modified April 1, 1990. Version 1.
Checksum: EA041C1C45A5777F

FASTA33537,717
        10         20         30         40         50         60 
MGCLLFLLLW ALLQAWGSAE VPQRLFPLRC LQISSFANSS WTRTDGLAWL GELQTHSWSN 

        70         80         90        100        110        120 
DSDTVRSLKP WSQGTFSDQQ WETLQHIFRV YRSSFTRDVK EFAKMLRLSY PLELQVSAGC 

       130        140        150        160        170        180 
EVHPGNASNN FFHVAFQGKD ILSFQGTSWE PTQEAPLWVN LAIQVLNQDK WTRETVQWLL 

       190        200        210        220        230        240 
NGTCPQFVSG LLESGKSELK KQVKPKAWLS RGPSPGPGRL LLVCHVSGFY PKPVWVKWMR 

       250        260        270        280        290        300 
GEQEQQGTQP GDILPNADET WYLRATLDVV AGEAAGLSCR VKHSSLEGQD IVLYWGGSYT 

       310        320        330 
SMGLIALAVL ACLLFLLIVG FTSRFKRQTS YQGVL 

« Hide

References

« Hide 'large scale' references
[1]"Two classes of CD1 genes."
Calabi F., Jarvis J.M., Martin L., Milstein C.
Eur. J. Immunol. 19:285-292(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Isolation and characterization of a cDNA and gene coding for a fourth CD1 molecule."
Balk S.P., Bleicher P.A., Terhorst C.
Proc. Natl. Acad. Sci. U.S.A. 86:252-256(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA].
[3]"The DNA sequence and biological annotation of human chromosome 1."
Gregory S.G., Barlow K.F., McLay K.E., Kaul R., Swarbreck D., Dunham A., Scott C.E., Howe K.L., Woodfine K., Spencer C.C.A., Jones M.C., Gillson C., Searle S., Zhou Y., Kokocinski F., McDonald L., Evans R., Phillips K. expand/collapse author list , Atkinson A., Cooper R., Jones C., Hall R.E., Andrews T.D., Lloyd C., Ainscough R., Almeida J.P., Ambrose K.D., Anderson F., Andrew R.W., Ashwell R.I.S., Aubin K., Babbage A.K., Bagguley C.L., Bailey J., Beasley H., Bethel G., Bird C.P., Bray-Allen S., Brown J.Y., Brown A.J., Buckley D., Burton J., Bye J., Carder C., Chapman J.C., Clark S.Y., Clarke G., Clee C., Cobley V., Collier R.E., Corby N., Coville G.J., Davies J., Deadman R., Dunn M., Earthrowl M., Ellington A.G., Errington H., Frankish A., Frankland J., French L., Garner P., Garnett J., Gay L., Ghori M.R.J., Gibson R., Gilby L.M., Gillett W., Glithero R.J., Grafham D.V., Griffiths C., Griffiths-Jones S., Grocock R., Hammond S., Harrison E.S.I., Hart E., Haugen E., Heath P.D., Holmes S., Holt K., Howden P.J., Hunt A.R., Hunt S.E., Hunter G., Isherwood J., James R., Johnson C., Johnson D., Joy A., Kay M., Kershaw J.K., Kibukawa M., Kimberley A.M., King A., Knights A.J., Lad H., Laird G., Lawlor S., Leongamornlert D.A., Lloyd D.M., Loveland J., Lovell J., Lush M.J., Lyne R., Martin S., Mashreghi-Mohammadi M., Matthews L., Matthews N.S.W., McLaren S., Milne S., Mistry S., Moore M.J.F., Nickerson T., O'Dell C.N., Oliver K., Palmeiri A., Palmer S.A., Parker A., Patel D., Pearce A.V., Peck A.I., Pelan S., Phelps K., Phillimore B.J., Plumb R., Rajan J., Raymond C., Rouse G., Saenphimmachak C., Sehra H.K., Sheridan E., Shownkeen R., Sims S., Skuce C.D., Smith M., Steward C., Subramanian S., Sycamore N., Tracey A., Tromans A., Van Helmond Z., Wall M., Wallis J.M., White S., Whitehead S.L., Wilkinson J.E., Willey D.L., Williams H., Wilming L., Wray P.W., Wu Z., Coulson A., Vaudin M., Sulston J.E., Durbin R.M., Hubbard T., Wooster R., Dunham I., Carter N.P., McVean G., Ross M.T., Harrow J., Olson M.V., Beck S., Rogers J., Bentley D.R.
Nature 441:315-321(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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].
Tissue: Pancreas.
[6]"Polymorphism of human CD1 genes."
Han M., Hannick L.I., DiBrino M., Robinson M.A.
Tissue Antigens 54:122-127(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-109, VARIANT SER-64.
[7]"Isolation of CD1 genes: a family of major histocompatibility complex-related differentiation antigens."
Martin L.H., Calabi F., Milstein C.
Proc. Natl. Acad. Sci. U.S.A. 83:9154-9158(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 203-295.
[8]"A critical tyrosine residue in the cytoplasmic tail is important for CD1d internalization but not for its basolateral sorting in MDCK cells."
Rodionov D.G., Nordeng T.W., Pedersen K., Balk S.P., Bakke O.
J. Immunol. 162:1488-1495(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF TYR-331 AND VAL-334.
[9]"Regulation of intracellular trafficking of human CD1d by association with MHC class II molecules."
Kang S.-J., Cresswell P.
EMBO J. 21:1650-1660(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION, INTERACTION WITH B2M AND MHC II.
[10]"CD1d ligands: the good, the bad, and the ugly."
Brutkiewicz R.R.
J. Immunol. 177:769-775(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[11]"Distinct endosomal trafficking requirements for presentation of autoantigens and exogenous lipids by human CD1d molecules."
Chen X., Wang X., Keaton J.M., Reddington F., Illarionov P.A., Besra G.S., Gumperz J.E.
J. Immunol. 178:6181-6190(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[12]"Mass-spectrometric identification and relative quantification of N-linked cell surface glycoproteins."
Wollscheid B., Bausch-Fluck D., Henderson C., O'Brien R., Bibel M., Schiess R., Aebersold R., Watts J.D.
Nat. Biotechnol. 27:378-386(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-60.
Tissue: Leukemic T-cell.
[13]"The crystal structure of human CD1d with and without alpha-galactosylceramide."
Koch M., Stronge V.S., Shepherd D., Gadola S.D., Mathew B., Ritter G., Fersht A.R., Besra G.S., Schmidt R.R., Jones E.Y., Cerundolo V.
Nat. Immunol. 6:819-826(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 19-299 IN COMPLEX WITH B2M AND GALACTOSYLCERAMIDE, DISULFIDE BONDS.
[14]"CD1d-lipid-antigen recognition by the semi-invariant NKT T-cell receptor."
Borg N.A., Wun K.S., Kjer-Nielsen L., Wilce M.C.J., Pellicci D.G., Koh R., Besra G.S., Bharadwaj M., Godfrey D.I., McCluskey J., Rossjohn J.
Nature 448:44-49(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.2 ANGSTROMS) OF 24-295 IN COMPLEX WITH B2M AND T-CELL RECEPTOR, GLYCOSYLATION AT ASN-38 AND ASN-60.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
L38820 expand/collapse EMBL AC list , L38815, L38817, L38816, L38818, L38819 Genomic DNA. Translation: AAA59672.1.
X14974 Genomic DNA. Translation: CAA33099.1.
J04142 mRNA. Translation: AAA59673.1.
AL138899 Genomic DNA. Translation: CAH73515.1.
CH471121 Genomic DNA. Translation: EAW52847.1.
CH471121 Genomic DNA. Translation: EAW52848.1.
CH471121 Genomic DNA. Translation: EAW52849.1.
BC027926 mRNA. Translation: AAH27926.1.
AF142668 Genomic DNA. Translation: AAD37581.1.
M14664 Genomic DNA. Translation: AAA51935.1.
PIRHLHUR3. S07715.
RefSeqNP_001757.1. NM_001766.3.
UniGeneHs.1799.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1ZT4X-ray3.00A/C19-299[»]
2PO6X-ray3.20A/E24-295[»]
3HUJX-ray2.50A/C21-295[»]
3SDXX-ray3.12A/C24-295[»]
3TZVX-ray3.06C21-295[»]
3U0PX-ray2.80A/C/E21-295[»]
3VWJX-ray3.09A21-295[»]
3VWKX-ray2.94A21-295[»]
4EN3X-ray2.57C21-295[»]
4LHUX-ray2.87A24-295[»]
4MNGX-ray3.01A/C21-201[»]
4MQ7X-ray2.60A21-202[»]
ProteinModelPortalP15813.
SMRP15813. Positions 23-295.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107350. 5 interactions.
DIPDIP-60257N.
STRING9606.ENSP00000357153.

Chemistry

ChEMBLCHEMBL1649053.

PTM databases

PhosphoSiteP15813.

Polymorphism databases

DMDM115964.

Proteomic databases

PaxDbP15813.
PRIDEP15813.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000368171; ENSP00000357153; ENSG00000158473.
GeneID912.
KEGGhsa:912.
UCSCuc001frr.3. human.

Organism-specific databases

CTD912.
GeneCardsGC01P158149.
HGNCHGNC:1637. CD1D.
HPACAB016107.
MIM188410. gene.
neXtProtNX_P15813.
PharmGKBPA26196.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG26626.
HOGENOMHOG000111666.
HOVERGENHBG004453.
InParanoidP15813.
KOK06448.
OMALNDTCPQ.
OrthoDBEOG7DZ8K9.
PhylomeDBP15813.
TreeFamTF336723.

Gene expression databases

BgeeP15813.
CleanExHS_CD1D.
GenevestigatorP15813.

Family and domain databases

Gene3D2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProIPR007110. Ig-like_dom.
IPR013783. Ig-like_fold.
IPR003597. Ig_C1-set.
IPR011161. MHC_I-like_Ag-recog.
IPR011162. MHC_I/II-like_Ag-recog.
[Graphical view]
PfamPF07654. C1-set. 1 hit.
[Graphical view]
SMARTSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMSSF54452. SSF54452. 1 hit.
PROSITEPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP15813.
GeneWikiCD1D.
GenomeRNAi912.
NextBio3762.
PROP15813.
SOURCESearch...

Entry information

Entry nameCD1D_HUMAN
AccessionPrimary (citable) accession number: P15813
Secondary accession number(s): D3DVD5 expand/collapse secondary AC list , Q5W0J3, Q9UMM3, Q9Y5M4
Entry history
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: April 16, 2014
This is version 145 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 1

Human chromosome 1: entries, gene names and cross-references to MIM

Human cell differentiation molecules

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