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Protein

Antigen-presenting glycoprotein CD1d

Gene

CD1D

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

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

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

GO - Biological processi

Keywordsi

Biological processImmunity, Innate immunity

Enzyme and pathway databases

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

EuPathDBiHostDB:ENSG00000158473.6
HGNCiHGNC:1637 CD1D
MIMi188410 gene
neXtProtiNX_P15813

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Topology

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

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
DrugBankiDB04661 Cis-tetracosenoyl sulfatide

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...) asparagine1 Publication1
Glycosylationi60N-linked (GlcNAc...) asparagine2 Publications1
Disulfide bondi120 ↔ 184Combined sources2 Publications
Glycosylationi126N-linked (GlcNAc...) asparagineSequence analysis1
Glycosylationi181N-linked (GlcNAc...) asparagineSequence analysis1
Disulfide bondi224 ↔ 279Combined sources2 Publications

Keywords - PTMi

Disulfide bond, Glycoprotein

Proteomic databases

MaxQBiP15813
PaxDbiP15813
PeptideAtlasiP15813
PRIDEiP15813
ProteomicsDBi53222

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 Expressed in 130 organ(s), highest expression level in leukocyte
CleanExiHS_CD1D
GenevisibleiP15813 HS

Organism-specific databases

HPAiCAB016107
HPA072662

Interactioni

Subunit structurei

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

GO - Molecular functioni

Protein-protein interaction databases

BioGridi107350, 6 interactors
DIPiDIP-60257N
IntActiP15813, 1 interactor
STRINGi9606.ENSP00000357153

Structurei

Secondary structure

1335
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

Keywords - Domaini

Immunoglobulin domain, Signal, Transmembrane, Transmembrane helix

Phylogenomic databases

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

Family and domain databases

Gene3Di2.60.40.10, 1 hit
3.30.500.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003597 Ig_C1-set
IPR011161 MHC_I-like_Ag-recog
IPR037055 MHC_I-like_Ag-recog_sf
IPR011162 MHC_I/II-like_Ag-recog
PfamiView protein in Pfam
PF07654 C1-set, 1 hit
PF16497 MHC_I_3, 1 hit
SMARTiView protein in SMART
SM00407 IGc1, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
SSF54452 SSF54452, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit

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 → S1 PublicationCorresponds to variant dbSNP:rs62621276Ensembl.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 No translation available.
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

Similar proteinsi

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 No translation available.
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, 6 interactors
DIPiDIP-60257N
IntActiP15813, 1 interactor
STRINGi9606.ENSP00000357153

Chemistry databases

ChEMBLiCHEMBL1649053
DrugBankiDB04661 Cis-tetracosenoyl sulfatide

PTM databases

iPTMnetiP15813
PhosphoSitePlusiP15813

Polymorphism and mutation databases

BioMutaiCD1D
DMDMi115964

Proteomic databases

MaxQBiP15813
PaxDbiP15813
PeptideAtlasiP15813
PRIDEiP15813
ProteomicsDBi53222

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

CTDi912
DisGeNETi912
EuPathDBiHostDB:ENSG00000158473.6
GeneCardsiCD1D
HGNCiHGNC:1637 CD1D
HPAiCAB016107
HPA072662
MIMi188410 gene
neXtProtiNX_P15813
OpenTargetsiENSG00000158473
PharmGKBiPA26196
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

ReactomeiR-HSA-198933 Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell

Miscellaneous databases

EvolutionaryTraceiP15813
GeneWikiiCD1D
GenomeRNAii912
PROiPR:P15813
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000158473 Expressed in 130 organ(s), highest expression level in leukocyte
CleanExiHS_CD1D
GenevisibleiP15813 HS

Family and domain databases

Gene3Di2.60.40.10, 1 hit
3.30.500.10, 1 hit
InterProiView protein in InterPro
IPR007110 Ig-like_dom
IPR036179 Ig-like_dom_sf
IPR013783 Ig-like_fold
IPR003597 Ig_C1-set
IPR011161 MHC_I-like_Ag-recog
IPR037055 MHC_I-like_Ag-recog_sf
IPR011162 MHC_I/II-like_Ag-recog
PfamiView protein in Pfam
PF07654 C1-set, 1 hit
PF16497 MHC_I_3, 1 hit
SMARTiView protein in SMART
SM00407 IGc1, 1 hit
SUPFAMiSSF48726 SSF48726, 1 hit
SSF54452 SSF54452, 1 hit
PROSITEiView protein in PROSITE
PS50835 IG_LIKE, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiCD1D_HUMAN
AccessioniPrimary (citable) accession number: P15813
Secondary accession number(s): D3DVD5
, Q5W0J3, Q9UMM3, Q9Y5M4
Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1990
Last sequence update: April 1, 1990
Last modified: November 7, 2018
This is version 184 of the entry and version 1 of the sequence. See 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

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

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

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