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P15813

- CD1D_HUMAN

UniProt

P15813 - CD1D_HUMAN

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Protein

Antigen-presenting glycoprotein CD1d

Gene

CD1D

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

Functioni

Antigen-presenting protein that binds self and non-self glycolipids and presents them to T-cell receptors on natural killer T-cells.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei98 – 981Glycolipid
Binding sitei169 – 1691Glycolipid
Binding sitei172 – 1721Glycolipid

GO - Molecular functioni

  1. beta-2-microglobulin binding Source: UniProtKB
  2. cell adhesion molecule binding Source: BHF-UCL
  3. exogenous lipid antigen binding Source: UniProtKB
  4. histone binding Source: UniProtKB
  5. lipid antigen binding Source: BHF-UCL
  6. receptor activity Source: UniProtKB

GO - Biological processi

  1. antigen processing and presentation, endogenous lipid antigen via MHC class Ib Source: UniProtKB
  2. detection of bacterium Source: UniProtKB
  3. heterotypic cell-cell adhesion Source: BHF-UCL
  4. innate immune response Source: UniProtKB-KW
  5. positive regulation of innate immune response Source: UniProtKB
  6. positive regulation of T cell proliferation Source: BHF-UCL
  7. T cell selection Source: UniProtKB
  8. viral process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, Immunity, Innate immunity

Names & Taxonomyi

Protein namesi
Recommended name:
Antigen-presenting glycoprotein CD1d
Alternative name(s):
R3G1
CD_antigen: CD1d
Gene namesi
Name:CD1D
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640: Chromosome 1

Organism-specific databases

HGNCiHGNC:1637. CD1D.

Subcellular locationi

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

GO - Cellular componenti

  1. cell surface Source: BHF-UCL
  2. cytoplasm Source: BHF-UCL
  3. endosome Source: UniProtKB-KW
  4. integral component of plasma membrane Source: UniProtKB
  5. lysosome Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endosome, Lysosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi331 – 3311Y → A: Strongly reduced internalization. 1 Publication
Mutagenesisi334 – 3341V → A: Strongly reduced internalization. 1 Publication

Organism-specific databases

PharmGKBiPA26196.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 1919Sequence AnalysisAdd
BLAST
Chaini20 – 335316Antigen-presenting glycoprotein CD1dPRO_0000014581Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi38 – 381N-linked (GlcNAc...)1 Publication
Glycosylationi60 – 601N-linked (GlcNAc...)2 Publications
Disulfide bondi120 ↔ 1841 PublicationPROSITE-ProRule annotation
Glycosylationi126 – 1261N-linked (GlcNAc...)Sequence Analysis
Glycosylationi181 – 1811N-linked (GlcNAc...)Sequence Analysis
Disulfide bondi224 ↔ 2791 PublicationPROSITE-ProRule annotation

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiP15813.
PaxDbiP15813.
PRIDEiP15813.

PTM databases

PhosphoSiteiP15813.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiP15813.
CleanExiHS_CD1D.
GenevestigatoriP15813.

Organism-specific databases

HPAiCAB016107.

Interactioni

Subunit structurei

Heterodimer with B2M (beta-2-microglobulin). Interacts with MHC II.3 Publications

Protein-protein interaction databases

BioGridi107350. 5 interactions.
DIPiDIP-60257N.
STRINGi9606.ENSP00000357153.

Structurei

Secondary structure

1
335
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi28 – 3811
Beta strandi41 – 5010
Beta strandi53 – 586
Beta strandi63 – 675
Turni70 – 756
Helixi78 – 10528
Beta strandi112 – 12211
Beta strandi124 – 1263
Beta strandi128 – 1369
Beta strandi139 – 1457
Beta strandi148 – 1514
Helixi158 – 1669
Helixi170 – 18112
Helixi183 – 19412
Helixi196 – 1994
Beta strandi206 – 2116
Beta strandi216 – 23217
Beta strandi235 – 2406
Beta strandi241 – 2433
Beta strandi248 – 2503
Turni257 – 2593
Beta strandi261 – 27212
Beta strandi278 – 2825
Turni284 – 2874
Beta strandi291 – 2944

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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[»]
ProteinModelPortaliP15813.
SMRiP15813. Positions 23-295.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15813.

Topological domain

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini20 – 301282ExtracellularSequence AnalysisAdd
BLAST
Topological domaini323 – 33513CytoplasmicSequence AnalysisAdd
BLAST

Transmembrane

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei302 – 32221HelicalSequence AnalysisAdd
BLAST

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini185 – 292108Ig-likeAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi331 – 3344Internalization signal

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiNOG26626.
GeneTreeiENSGT00480000042665.
HOGENOMiHOG000111666.
HOVERGENiHBG004453.
InParanoidiP15813.
KOiK06448.
OMAiLNDTCPQ.
OrthoDBiEOG7DZ8K9.
PhylomeDBiP15813.
TreeFamiTF336723.

Family and domain databases

Gene3Di2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProiIPR007110. 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]
PfamiPF07654. C1-set. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMiSSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P15813-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MGCLLFLLLW ALLQAWGSAE VPQRLFPLRC LQISSFANSS WTRTDGLAWL
60 70 80 90 100
GELQTHSWSN DSDTVRSLKP WSQGTFSDQQ WETLQHIFRV YRSSFTRDVK
110 120 130 140 150
EFAKMLRLSY PLELQVSAGC EVHPGNASNN FFHVAFQGKD ILSFQGTSWE
160 170 180 190 200
PTQEAPLWVN LAIQVLNQDK WTRETVQWLL NGTCPQFVSG LLESGKSELK
210 220 230 240 250
KQVKPKAWLS RGPSPGPGRL LLVCHVSGFY PKPVWVKWMR GEQEQQGTQP
260 270 280 290 300
GDILPNADET WYLRATLDVV AGEAAGLSCR VKHSSLEGQD IVLYWGGSYT
310 320 330
SMGLIALAVL ACLLFLLIVG FTSRFKRQTS YQGVL
Length:335
Mass (Da):37,717
Last modified:April 1, 1990 - v1
Checksum:iEA041C1C45A5777F
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti64 – 641T → S.1 Publication
Corresponds to variant rs62621276 [ dbSNP | Ensembl ].
VAR_010211

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
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.
CCDSiCCDS1173.1.
PIRiS07715. HLHUR3.
RefSeqiNP_001757.1. NM_001766.3.
UniGeneiHs.1799.
Hs.731511.

Genome annotation databases

EnsembliENST00000368171; ENSP00000357153; ENSG00000158473.
GeneIDi912.
KEGGihsa:912.
UCSCiuc001frr.3. human.

Polymorphism databases

DMDMi115964.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
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 .
CCDSi CCDS1173.1.
PIRi S07715. HLHUR3.
RefSeqi NP_001757.1. NM_001766.3.
UniGenei Hs.1799.
Hs.731511.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
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 [» ]
3SDX X-ray 3.12 A/C 24-295 [» ]
3TZV X-ray 3.06 C 21-295 [» ]
3U0P X-ray 2.80 A/C/E 21-295 [» ]
3VWJ X-ray 3.09 A 21-295 [» ]
3VWK X-ray 2.94 A 21-295 [» ]
4EN3 X-ray 2.57 C 21-295 [» ]
4LHU X-ray 2.87 A 24-295 [» ]
4MNG X-ray 3.01 A/C 21-201 [» ]
4MQ7 X-ray 2.60 A 21-202 [» ]
ProteinModelPortali P15813.
SMRi P15813. Positions 23-295.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 107350. 5 interactions.
DIPi DIP-60257N.
STRINGi 9606.ENSP00000357153.

Chemistry

ChEMBLi CHEMBL1649053.

PTM databases

PhosphoSitei P15813.

Polymorphism databases

DMDMi 115964.

Proteomic databases

MaxQBi P15813.
PaxDbi P15813.
PRIDEi P15813.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

Ensembli ENST00000368171 ; ENSP00000357153 ; ENSG00000158473 .
GeneIDi 912.
KEGGi hsa:912.
UCSCi uc001frr.3. human.

Organism-specific databases

CTDi 912.
GeneCardsi GC01P158149.
HGNCi HGNC:1637. CD1D.
HPAi CAB016107.
MIMi 188410. gene.
neXtProti NX_P15813.
PharmGKBi PA26196.
GenAtlasi Search...

Phylogenomic databases

eggNOGi NOG26626.
GeneTreei ENSGT00480000042665.
HOGENOMi HOG000111666.
HOVERGENi HBG004453.
InParanoidi P15813.
KOi K06448.
OMAi LNDTCPQ.
OrthoDBi EOG7DZ8K9.
PhylomeDBi P15813.
TreeFami TF336723.

Miscellaneous databases

EvolutionaryTracei P15813.
GeneWikii CD1D.
GenomeRNAii 912.
NextBioi 3762.
PROi P15813.
SOURCEi Search...

Gene expression databases

Bgeei P15813.
CleanExi HS_CD1D.
Genevestigatori P15813.

Family and domain databases

Gene3Di 2.60.40.10. 1 hit.
3.30.500.10. 1 hit.
InterProi IPR007110. 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 ]
Pfami PF07654. C1-set. 1 hit.
[Graphical view ]
SMARTi SM00407. IGc1. 1 hit.
[Graphical view ]
SUPFAMi SSF54452. SSF54452. 1 hit.
PROSITEi PS50835. IG_LIKE. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  1. 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.
    , 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. 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. 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. Cited for: X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS) OF 19-299 IN COMPLEX WITH B2M AND GALACTOSYLCERAMIDE, DISULFIDE BONDS.
  14. 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.

Entry informationi

Entry nameiCD1D_HUMAN
AccessioniPrimary (citable) accession number: P15813
Secondary accession number(s): D3DVD5
, Q5W0J3, Q9UMM3, Q9Y5M4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: October 29, 2014
This is version 149 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (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.

Miscellaneousi

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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human cell differentiation molecules
    CD nomenclature of surface proteins of human leucocytes and list of entries
  2. Human chromosome 1
    Human chromosome 1: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  7. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3