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Protein

Antigen-presenting glycoprotein CD1d

Gene

CD1D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: 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)DescriptionActionsGraphical viewLength
Binding sitei98GlycolipidCombined sources2 Publications1

GO - Molecular functioni

  • beta-2-microglobulin binding Source: UniProtKB
  • cell adhesion molecule binding Source: BHF-UCL
  • endogenous lipid antigen binding Source: GO_Central
  • exogenous lipid antigen binding Source: UniProtKB
  • histone binding Source: UniProtKB
  • lipid antigen binding Source: BHF-UCL
  • lipopeptide binding Source: GO_Central
  • receptor activity Source: UniProtKB

GO - Biological processi

  • antigen processing and presentation, endogenous lipid antigen via MHC class Ib Source: UniProtKB
  • antigen processing and presentation, exogenous lipid antigen via MHC class Ib Source: GO_Central
  • detection of bacterium Source: UniProtKB
  • heterotypic cell-cell adhesion Source: BHF-UCL
  • innate immune response Source: UniProtKB-KW
  • positive regulation of innate immune response Source: UniProtKB
  • positive regulation of T cell proliferation Source: BHF-UCL
  • regulation of immune response Source: Reactome
  • T cell selection Source: UniProtKB
  • viral process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

Host-virus interaction, Immunity, Innate immunity

Enzyme and pathway databases

BioCyciZFISH:ENSG00000158473-MONOMER.
ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.

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
Proteomesi
  • UP000005640 Componenti: Chromosome 1

Organism-specific databases

HGNCiHGNC:1637. CD1D.

Subcellular locationi

  • Cell membrane 3 Publications; Single-pass type I membrane protein 1 Publication
  • Basolateral cell membrane 1 Publication; Single-pass type I membrane protein 1 Publication
  • Endosome membrane 2 Publications; Single-pass type I membrane protein 1 Publication
  • Lysosome membrane 2 Publications; Single-pass type I membrane protein 1 Publication
  • Endoplasmic reticulum membrane 1 Publication; Single-pass type I membrane protein 1 Publication

  • Note: Subject to intracellular trafficking between the cell membrane, endosomes and lysosomes.1 Publication

Topology

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Topological domaini20 – 301ExtracellularSequence analysisAdd BLAST282
Transmembranei302 – 322HelicalSequence analysisAdd BLAST21
Topological domaini323 – 335CytoplasmicSequence analysisAdd BLAST13

GO - Cellular componenti

  • basolateral plasma membrane Source: UniProtKB-SubCell
  • cell surface Source: BHF-UCL
  • cytoplasm Source: BHF-UCL
  • endoplasmic reticulum membrane Source: UniProtKB-SubCell
  • endosome membrane Source: UniProtKB-SubCell
  • integral component of plasma membrane Source: UniProtKB
  • lysosomal membrane Source: UniProtKB-SubCell
  • plasma membrane Source: Reactome
Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Endoplasmic reticulum, Endosome, Lysosome, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi331Y → A: Strongly reduced internalization. 1 Publication1
Mutagenesisi334V → A: Strongly reduced internalization. 1 Publication1

Organism-specific databases

DisGeNETi912.
OpenTargetsiENSG00000158473.
PharmGKBiPA26196.

Chemistry databases

ChEMBLiCHEMBL1649053.

Polymorphism and mutation databases

BioMutaiCD1D.
DMDMi115964.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Signal peptidei1 – 19Sequence analysisAdd BLAST19
ChainiPRO_000001458120 – 335Antigen-presenting glycoprotein CD1dAdd BLAST316

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Glycosylationi38N-linked (GlcNAc...)1 Publication1
Glycosylationi60N-linked (GlcNAc...)2 Publications1
Disulfide bondi120 ↔ 184Combined sources2 Publications
Glycosylationi126N-linked (GlcNAc...)Sequence analysis1
Glycosylationi181N-linked (GlcNAc...)Sequence analysis1
Disulfide bondi224 ↔ 279Combined sources2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

EPDiP15813.
MaxQBiP15813.
PaxDbiP15813.
PeptideAtlasiP15813.
PRIDEiP15813.

PTM databases

iPTMnetiP15813.
PhosphoSitePlusiP15813.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000158473.
CleanExiHS_CD1D.
GenevisibleiP15813. HS.

Organism-specific databases

HPAiCAB016107.

Interactioni

Subunit structurei

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

GO - Molecular functioni

  • beta-2-microglobulin binding Source: UniProtKB
  • cell adhesion molecule binding Source: BHF-UCL
  • histone binding Source: UniProtKB

Protein-protein interaction databases

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

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi28 – 40Combined sources13
Beta strandi42 – 50Combined sources9
Beta strandi53 – 58Combined sources6
Beta strandi63 – 67Combined sources5
Turni70 – 75Combined sources6
Helixi78 – 105Combined sources28
Beta strandi110 – 121Combined sources12
Beta strandi124 – 126Combined sources3
Beta strandi129 – 136Combined sources8
Beta strandi139 – 145Combined sources7
Beta strandi148 – 151Combined sources4
Helixi157 – 166Combined sources10
Helixi170 – 181Combined sources12
Helixi183 – 194Combined sources12
Helixi196 – 199Combined sources4
Beta strandi206 – 212Combined sources7
Beta strandi215 – 232Combined sources18
Beta strandi235 – 240Combined sources6
Beta strandi241 – 243Combined sources3
Beta strandi248 – 250Combined sources3
Turni257 – 259Combined sources3
Beta strandi261 – 270Combined sources10
Turni271 – 276Combined sources6
Beta strandi278 – 282Combined sources5
Helixi284 – 286Combined sources3
Beta strandi291 – 294Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4WO4X-ray2.50A24-295[»]
4WW2X-ray2.48C21-295[»]
4WWKX-ray3.10C21-295[»]
ProteinModelPortaliP15813.
SMRiP15813.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP15813.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini185 – 292Ig-likeAdd BLAST108

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni169 – 172Glycolipid bindingCombined sources2 Publications4

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi331 – 334Internalization signal4

Sequence similaritiesi

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410ITUC. Eukaryota.
ENOG4111EG6. LUCA.
GeneTreeiENSGT00480000042665.
HOGENOMiHOG000111666.
HOVERGENiHBG004453.
InParanoidiP15813.
KOiK06448.
OMAiRQTSYQG.
OrthoDBiEOG091G0H36.
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.
PF16497. MHC_I_3. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF54452. 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)DescriptionActionsGraphical viewLength
Natural variantiVAR_01021164T → S.1 PublicationCorresponds to variant rs62621276dbSNPEnsembl.1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001306074.1. NM_001319145.1.
NP_001757.1. NM_001766.3.
XP_011508427.1. XM_011510125.1.
UniGeneiHs.1799.
Hs.731511.

Genome annotation databases

EnsembliENST00000368171; ENSP00000357153; ENSG00000158473.
GeneIDi912.
KEGGihsa:912.
UCSCiuc001frr.4. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_001306074.1. NM_001319145.1.
NP_001757.1. NM_001766.3.
XP_011508427.1. XM_011510125.1.
UniGeneiHs.1799.
Hs.731511.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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[»]
4WO4X-ray2.50A24-295[»]
4WW2X-ray2.48C21-295[»]
4WWKX-ray3.10C21-295[»]
ProteinModelPortaliP15813.
SMRiP15813.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry databases

ChEMBLiCHEMBL1649053.

PTM databases

iPTMnetiP15813.
PhosphoSitePlusiP15813.

Polymorphism and mutation databases

BioMutaiCD1D.
DMDMi115964.

Proteomic databases

EPDiP15813.
MaxQBiP15813.
PaxDbiP15813.
PeptideAtlasiP15813.
PRIDEiP15813.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000368171; ENSP00000357153; ENSG00000158473.
GeneIDi912.
KEGGihsa:912.
UCSCiuc001frr.4. human.

Organism-specific databases

CTDi912.
DisGeNETi912.
GeneCardsiCD1D.
HGNCiHGNC:1637. CD1D.
HPAiCAB016107.
MIMi188410. gene.
neXtProtiNX_P15813.
OpenTargetsiENSG00000158473.
PharmGKBiPA26196.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410ITUC. Eukaryota.
ENOG4111EG6. LUCA.
GeneTreeiENSGT00480000042665.
HOGENOMiHOG000111666.
HOVERGENiHBG004453.
InParanoidiP15813.
KOiK06448.
OMAiRQTSYQG.
OrthoDBiEOG091G0H36.
PhylomeDBiP15813.
TreeFamiTF336723.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000158473-MONOMER.
ReactomeiR-HSA-198933. Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell.

Miscellaneous databases

EvolutionaryTraceiP15813.
GeneWikiiCD1D.
GenomeRNAii912.
PROiP15813.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000158473.
CleanExiHS_CD1D.
GenevisibleiP15813. HS.

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.
PF16497. MHC_I_3. 1 hit.
[Graphical view]
SMARTiSM00407. IGc1. 1 hit.
[Graphical view]
SUPFAMiSSF48726. SSF48726. 1 hit.
SSF54452. SSF54452. 1 hit.
PROSITEiPS50835. IG_LIKE. 1 hit.
[Graphical view]
ProtoNetiSearch...

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: November 2, 2016
This is version 169 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.