CD1D CD1d molecule [Homo sapiens] - Gene

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Summary

Official Symbol: CD1Dprovided by HGNC
Official Full Name: CD1d moleculeprovided by HGNC
Primary source: HGNC:1637
See related: Ensembl:ENSG00000158473; HPRD:01780; MIM:188410; Vega:OTTHUMG00000022436
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: R3; CD1A; MGC34622
Summary: This gene encodes a divergent member of the CD1 family of transmembrane glycoproteins, which are structurally related to the major histocompatibility complex (MHC) proteins and form heterodimers with beta-2-microglobulin. The CD1 proteins mediate the presentation of primarily lipid and glycolipid antigens of self or microbial origin to T cells. The human genome contains five CD1 family genes organized in a cluster on chromosome 1. The CD1 family members are thought to differ in their cellular localization and specificity for particular lipid ligands. The protein encoded by this gene localizes to late endosomes and lysosomes via a tyrosine-based motif in the cytoplasmic tail. [provided by RefSeq, Jul 2008]

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Genomic context

Location :: 1q22-q23

Sequence :: Chromosome: 1; NC_000001.10 (158149737..158156217)

See CD1D in Epigenomics, MapViewer

Chromosome 1 - NC_000001.10 Genomic Context describing neighboring genes

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Genomic regions, transcripts, and products

Genomic Sequence

Go to nucleotideGraphics FASTA GenBank

Go to reference sequence details

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Bibliography

GeneRIFs: Gene References Into Functions What's a GeneRIF?

Defective B cell-mediated stimulation of iNKT cells in SLE patients was associated with altered CD1d recycling.
Title: Lipid-antigen presentation by CD1d(+) B cells is essential for the maintenance of invariant natural killer T cells.
The serine-containing variant showed the strongest CD1d binding, offering an explanation for its predominance in vivo.
Title: Natural variations at position 93 of the invariant Vα24-Jα18 α chain of human iNKT-cell TCRs strongly impact on CD1d binding.
CD1d appears to modulate some metabolic functions through an iNKT-independent mechanism
Title: Impact of CD1d deficiency on metabolism.
phenyl glycolipids showed greater binding avidity and stability for iNKT T-cell receptor when complexed with CD1d
Title: Avidity of CD1d-ligand-receptor ternary complex contributes to T-helper 1 (Th1) polarization and anticancer efficacy.
These findings provide the basis for investigations into a role for CD1d in lung mucosal immunity.
Title: Alternative spliced CD1d transcripts in human bronchial epithelial cells.
CD1d gene polymorphisms are associated with breast, colorectal and lung cancers.
Title: CD1a and CD1d genes polymorphisms in breast, colorectal and lung cancers.
Identification of self-lipids presented by CD1c and CD1d proteins.
Title: Identification of self-lipids presented by CD1c and CD1d proteins.
these results suggest that antigen presentation by CD1d is largely unaffected by the multiple immune-modulating functions of human cytomegalovirus.
Title: Human CD1d molecules are resistant to human cytomegalovirus US2- and US11-mediated degradation.
Breast cancer cells, through downregulation of CD1d and subsequent evasion of natural killer T-mediated antitumor immunity, gain increased potential for metastatic tumor progression.
Title: CD1d-expressing breast cancer cells modulate NKT cell-mediated antitumor immunity in a murine model of breast cancer metastasis.
CD1d can differentiate chronic lymphocytic leukemia from other B-cell chronic lymphoproliferative disorders with high accuracy.
Title: The diagnostic value of CD1d expression in a large cohort of patients with B-cell chronic lymphoproliferative disorders.

Submit: New GeneRIF Correction See all (83)

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Phenotypes

Review eQTL and phenotype association data in this region using PheGenI

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HIV-1 protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	CD1d surface expression on human cell lines is downregulated after infection with M-tropic HIV, T-tropic HIV, or after exposure to HIV gp120 in vitro	PubMed
Nef	nef	HIV-1 Nef-mediated downregulation of CD1d requires a tyrosine-based motif in the CD1d cytoplasmic tail and four Nef amino acid motifs (EEEE65, PxxP75, DD165, and LL175), which are known to be involved in the downregulation of MHC-I and CD4	PubMed
	nef	HIV-1 Nef downregulates the expression of the non-classical MHC-I like CD1d molecule by increasing internalization of CD1d molecules from the cell surface and retaining CD1d in the trans-Golgi-network (TGN)	PubMed
	nef	Nef-induced downregulation of CD1d is observed when cells are co-expressing Nef and CD1d, and six amino acids (300-305) in the cytoplasmic tail of CD1d are required for the downregulation by Nef	PubMed

Go to the HIV-1, Human Protein Interaction Database

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Products	Interactant	Other Gene	Source	Pubs	Description
P15813	P61769	B2M	HPRD	PubMed
P15813	P27797	CALR	HPRD	PubMed
P15813	P27824	CANX	HPRD	PubMed
P15813	P04233	CD74	HPRD	PubMed
P15813	P07237	P4HB	HPRD	PubMed
P15813	P08575	PTPRC	HPRD	PubMed
P15813	T cell antigen receptor, beta		HPRD	PubMed
BioGRID:107350	BioGRID:107044	B2M	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107350	BioGRID:107262	CALR	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107350	BioGRID:107271	CANX	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107350	BioGRID:120100	P4HTM	BioGRID	PubMed	Affinity Capture-Western
BioGRID:107350	BioGRID:111752	PTPRC	BioGRID	PubMed	Affinity Capture-Western

Function	Evidence Code	Pubs
beta-2-microglobulin binding	TAS Traceable Author Statement more info	PubMed
cell adhesion molecule binding	IPI Inferred from Physical Interaction more info	PubMed
eukaryotic cell surface binding	IDA Inferred from Direct Assay more info	PubMed
exogenous lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
histone binding	IPI Inferred from Physical Interaction more info
lipid antigen binding	IDA Inferred from Direct Assay more info	PubMed
receptor activity	IC Inferred by Curator more info	PubMed

Process	Evidence Code	Pubs
T cell selection	TAS Traceable Author Statement more info	PubMed
antigen processing and presentation	IEA Inferred from Electronic Annotation more info
antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IDA Inferred from Direct Assay more info	PubMed
detection of bacterium	TAS Traceable Author Statement more info	PubMed
heterotypic cell-cell adhesion	TAS Traceable Author Statement more info	PubMed
interspecies interaction between organisms	IEA Inferred from Electronic Annotation more info
positive regulation of T cell proliferation	IDA Inferred from Direct Assay more info	PubMed
positive regulation of innate immune response	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
cell surface	IDA Inferred from Direct Assay more info	PubMed
cytoplasm	IDA Inferred from Direct Assay more info	PubMed
endosome	IEA Inferred from Electronic Annotation more info
endosome membrane	IEA Inferred from Electronic Annotation more info
integral to plasma membrane	TAS Traceable Author Statement more info	PubMed
lysosomal membrane	IEA Inferred from Electronic Annotation more info
plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

Preferred Names: antigen-presenting glycoprotein CD1d

Names: antigen-presenting glycoprotein CD1d; R3G1; thymocyte antigen CD1D; CD1D antigen, d polypeptide; T-cell surface glycoprotein CD1d; differentiation antigen CD1-alpha-3; HMC class I antigen-like glycoprotein CD1D

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NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001766.3 → NP_001757.1 antigen-presenting glycoprotein CD1d precursor

Status: REVIEWED

Source sequence(s)

AL138899, BC027926, BX106524

Consensus CDS

CCDS1173.1

UniProtKB/Swiss-Prot

P15813

Related

ENSP00000357153, OTTHUMP00000024053, ENST00000368171, OTTHUMT00000058340

Conserved Domains (1) summary

cd07698
Location:203 – 295
Blast Score: 285

IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain

RefSeqs of Annotated Genomes: Build 37.3

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh37.p5 Primary Assembly

Genomic

NC_000001.10 Reference GRCh37.p5 Primary Assembly

Range

158149737..158156217

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

AC_000133.1 Alternate HuRef

Range

129508011..129514491

Download

GenBank, FASTA, Sequence Viewer (Graphics)

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Related Sequences

Nucleotide		Protein
Heading	Accession and Version	Protein
genomic	AF142668.1	AAD37581.1
genomic	AL138899.23	CAH73515.1
genomic	CH471121.2	EAW52847.1
		EAW52848.1
		EAW52849.1
genomic	L38816.1	AAA59672.1
genomic	L38817.1	AAA59672.1
genomic	L38818.1	AAA59672.1
genomic	L38819.1	AAA59672.1
genomic	L38820.1	AAA59672.1
genomic	M14664.1	AAA51935.1
genomic	X14974.1	CAA33099.1
mRNA	AK225996.1	None
mRNA	AK310749.1	None
mRNA	BC027926.1	AAH27926.1
mRNA	BX106524.1	None
mRNA	J04142.1	AAA59673.1