Reviewed, UniProtKB/Swiss-Prot P15813 (CD1D_HUMAN)

Names and origin

Protein names

Recommended name:
    T-cell surface glycoprotein CD1d
Alternative name(s):
    R3G1
    CD_antigen=CD1d

Gene names

Name:

CD1D

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	335 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	Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells. Ref.10
Subunit structure	Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II. Ref.8
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.10 Ref.8 Ref.7
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 process	Host-virus interaction Immune response Innate immunity
Cellular component	Cell membrane Endosome Lysosome Membrane
Coding sequence diversity	Polymorphism
Domain	Immunoglobulin domain Signal Transmembrane
PTM	Disulfide bond Glycoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	T cell selection Traceable author statement. Source: UniProtKB antigen processing and presentation, endogenous lipid antigen via MHC class Ib Inferred from direct assay. Source: UniProtKB detection of bacterium Traceable author statement. Source: UniProtKB innate immune response Inferred from electronic annotation. Source: UniProtKB-KW interspecies interaction between organisms Inferred from electronic annotation. Source: UniProtKB-KW positive regulation of innate immune response Traceable author statement. Source: UniProtKB
Cellular component	MHC class I protein complex Inferred from electronic annotation. Source: InterPro endosome membrane Inferred from electronic annotation. Source: UniProtKB-SubCell integral to plasma membrane Traceable author statement. Source: UniProtKB lysosomal membrane Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	beta-2-microglobulin binding Traceable author statement. Source: UniProtKB exogenous lipid antigen binding Inferred from direct assay. Source: UniProtKB 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 – 19

19

By similarity

Chain

20 – 335

316

T-cell surface glycoprotein CD1d

PRO_0000014581

Regions

Topological domain

20 – 301

282

Extracellular Potential

Transmembrane

302 – 322

21

Potential

Topological domain

323 – 335

13

Cytoplasmic Potential

Domain

185 – 292

108

Ig-like

Motif

331 – 334

4

Internalization signal

Sites

Binding site

98

1

Glycolipid

Binding site

169

1

Glycolipid

Binding site

172

1

Glycolipid

Amino acid modifications

Glycosylation

38

1

N-linked (GlcNAc...) Ref.13

Glycosylation

60

1

N-linked (GlcNAc...) Ref.13 Ref.11

Glycosylation

126

1

N-linked (GlcNAc...) Potential

Glycosylation

181

1

N-linked (GlcNAc...) Potential

Disulfide bond

120 ↔ 184

Ref.12

Disulfide bond

224 ↔ 279

Ref.12

Natural variations

Natural variant

64

1

T → S

VAR_010211

Experimental info

Mutagenesis

331

1

Y → A: Strongly reduced internalization. Ref.7

Mutagenesis

334

1

V → A: Strongly reduced internalization. Ref.7

Secondary structure

1

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335

Helix Strand Turn

Details...

Beta strand

28 – 38

11

Beta strand

41 – 50

10

Beta strand

53 – 58

6

Beta strand

60 – 64

5

Turn

70 – 75

6

Helix

78 – 105

28

Beta strand

110 – 122

13

Beta strand

124 – 126

3

Beta strand

128 – 136

9

Beta strand

139 – 145

7

Beta strand

148 – 151

4

Helix

158 – 166

9

Helix

172 – 181

10

Helix

183 – 199

17

Beta strand

206 – 212

7

Beta strand

215 – 219

5

Beta strand

221 – 232

12

Beta strand

235 – 237

3

Beta strand

241 – 243

3

Beta strand

261 – 268

8

Turn

271 – 273

3

Beta strand

278 – 282

5

Beta strand

286 – 288

3

Beta strand

291 – 294

4

Sequences

	Sequence		Length	Mass (Da)
	P15813-1 [UniParc]. Last modified April 1, 1990. Version 1. Checksum: EA041C1C45A5777F	FASTA	335	37,717
	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

References

	« Hide 'large scale' referencesShow '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: 2467814] [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: 2463622] [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. , 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: 16710414] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE 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: Pancreas.
[5]	"Polymorphism of human CD1 genes." Han M., Hannick L.I., DiBrino M., Robinson M.A. Tissue Antigens 54:122-127(1999) [PubMed: 10488738] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 19-109, VARIANT SER-64.
[6]	"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: 3097645] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 203-295.
[7]	"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: 9973405] [Abstract] Cited for: SUBCELLULAR LOCATION, MUTAGENESIS OF TYR-331 AND VAL-334.
[8]	"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: 11927549] [Abstract] Cited for: SUBCELLULAR LOCATION, INTERACTION WITH B2M AND MHC II.
[9]	"CD1d ligands: the good, the bad, and the ugly." Brutkiewicz R.R. J. Immunol. 177:769-775(2006) [PubMed: 16818729] [Abstract] Cited for: REVIEW.
[10]	"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: 17475845] [Abstract] Cited for: FUNCTION, SUBCELLULAR LOCATION.
[11]	"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: 19349973] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-60, MASS SPECTROMETRY.
[12]	"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: 16007090] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 19-299 IN COMPLEX WITH B2M AND GALACTOSYLCERAMIDE, DISULFIDE BONDS.
[13]	"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: 17581592] [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

EMBLGenBankDDBJ

L38820 , 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.
BC027926 mRNA. Translation: AAH27926.1.
AF142668 Genomic DNA. Translation: AAD37581.1.
M14664 Genomic DNA. Translation: AAA51935.1.

IPI

IPI00013435.

PIR

HLHUR3. S07715.

RefSeq

NP_001757.1.

UniGene

Hs.1799

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1ZT4	X-ray	3.00	A/C	19-299	[»]
2PO6	X-ray	3.20	A/E	24-295	[»]
3HUJ	X-ray	2.50	A/C	21-295	[»]

ModBase

Search...

Protein-protein interaction databases

STRING

P15813.

Proteomic databases

PRIDE

P15813.

Genome annotation databases

Ensembl

ENST00000368171; ENSP00000357153; ENSG00000158473; Homo sapiens. [Genome view]

GeneID

912.

KEGG

hsa:912.

UCSC

uc001frr.1. human.

Organism-specific databases

CTD

912.

GeneCards

GC01P156416.

HGNC

HGNC:1637. CD1D.

HPA

CAB016107.

MIM

188410. gene.

PharmGKB

PA26196.

GenAtlas

Search...

Phylogenomic databases

HOGENOM

HBG126245.

HOVERGEN

P15813.

InParanoid

P15813.

OMA

KQVKPKA.

OrthoDB

EOG96X1TH.

Gene expression databases

ArrayExpress

P15813.

Bgee

P15813.

CleanEx

HS_CD1D.

Genevestigator

P15813.

GermOnline

ENSG00000158473. Homo sapiens.

Family and domain databases

InterPro

IPR007110. Ig-like.
IPR003597. Ig_C1-set.
IPR011161. MHC_I-like_Ag-recog.
IPR011162. MHC_I/II-like_Ag-recog.
IPR001039. MHC_I_a_a1/a2.
[Graphical view]

Gene3D

G3DSA:3.30.500.10. MHC_I-like_Ag-recog. 1 hit.

Pfam

PF07654. C1-set. 1 hit.
PF00129. MHC_I. 1 hit.
[Graphical view]

SMART

SM00407. IGc1. 1 hit.
[Graphical view]

PROSITE

PS50835. IG_LIKE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other Resources

NextBio

3762.

SOURCE

Search...

Entry information

Entry name

CD1D_HUMAN

Accession

Primary (citable) accession number: P15813
Secondary accession number(s): Q5W0J3, Q9UMM3, Q9Y5M4

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1990
Last sequence update:	April 1, 1990
Last modified:	December 15, 2009
This is version 103 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.