CD1B CD1b molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD1Bprovided by HGNC
Official Full Name: CD1b moleculeprovided by HGNC
Primary source: HGNC:HGNC:1635
See related: Ensembl:ENSG00000158485 MIM:188360; AllianceGenome:HGNC:1635
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: R1; CD1; CD1A
Summary: This gene encodes a 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, and requires vesicular acidification to bind lipid antigens. [provided by RefSeq, Jul 2008]
Expression: Low expression observed in reference dataset See more
Orthologs: all
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Genomic context

Location:: 1q23.1

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (158285405..158331531, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (157422502..157468624, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (158297745..158301321, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CD4 and CD8 co-receptors modulate functional avidity of CD1b-restricted T cells.
Title: CD4 and CD8 co-receptors modulate functional avidity of CD1b-restricted T cells.
Synthetic mycobacterial diacyl trehaloses reveal differential recognition by human T cell receptors and the C-type lectin Mincle.
Title: Synthetic mycobacterial diacyl trehaloses reveal differential recognition by human T cell receptors and the C-type lectin Mincle.
Animal models for human group 1 CD1 protein function.
Title: Animal models for human group 1 CD1 protein function.
The miR-582/CD1B Axis Is Involved in Regulation of Dendritic Cells and Is Associated with Clinical Outcomes in Advanced Lung Adenocarcinoma.
Title: The miR-582/CD1B Axis Is Involved in Regulation of Dendritic Cells and Is Associated with Clinical Outcomes in Advanced Lung Adenocarcinoma.
this study provides evidence for cross-reactive CD1b-restricted T cell responses to bacterial and self-antigens, and identifies chemically defined targets for future discovery of self and foreign antigen cross-reactive T cells.
Title: CD1b presents self and Borrelia burgdorferi diacylglycerols to human T cells.
Sulfoglycolipids (SGLs) are uniquely synthesized by Mycobacterium tuberculosis. This study designed a novel hybrid synthesis of a naturally occurring SGL, generated CD1b tetramers loaded with natural or synthetic SGL analogs, and studied the molecular requirements for T cell receptor binding and T cell activation.
Title: CD1b Tetramers Identify T Cells that Recognize Natural and Synthetic Diacylated Sulfoglycolipids from Mycobacterium tuberculosis.
polyclonal germline-encoded mycolyl lipid-reactive T cell receptors that recognize CD1b-glucose-6-O-monomycolate use relatively conserved molecular mechanisms
Title: T cell receptor recognition of CD1b presenting a mycobacterial glycolipid.
the development of polyvalent complexes of CD1b proteins and carbohydrate backbones (dextramers) and their use in identifying CD1b autoreactive T cells from human donors.
Title: Human autoreactive T cells recognize CD1b and phospholipids.
[review] Humans express both Group 1 (CD1a, CD1b and CD1c) and Group 2 (CD1d) CD1 molecules with nonredundant functions in response to the presentation of endogenous lipids.
Title: Lipid presentation by human CD1 molecules and the diverse T cell populations that respond to them.
for isoforms CD1b through CD1e, our simulations show the near-complete collapse of the hydrophobic cavities in the absence of the antigen. This event results from the spontaneous closure of the binding domain entrance, flanked by two alpha-helices.
Title: Dynamics of the antigen-binding grooves in CD1 proteins: reversible hydrophobic collapse in the lipid-free state.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

PMC105497P1 (e-PCR)
- UniSTS:270117

NoName (e-PCR)
- UniSTS:481324

NoName (e-PCR)
- UniSTS:481893

NoName (e-PCR)
- UniSTS:489706

SHGC-12745 (e-PCR)
- UniSTS:30702

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables endogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables exogenous lipid antigen binding	IBA Inferred from Biological aspect of Ancestor more info
enables lipopeptide binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in antigen processing and presentation, endogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in antigen processing and presentation, exogenous lipid antigen via MHC class Ib	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of T cell mediated cytotoxicity	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
located_in cell surface	HDA more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in lysosomal membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	TAS Traceable Author Statement more info
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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Preferred Names: T-cell surface glycoprotein CD1b

Names: CD1B antigen, b polypeptide; cortical thymocyte antigen CD1B; differentiation antigen CD1-alpha-3

NCBI Reference Sequences (RefSeq)

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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_001764.3 → NP_001755.1 T-cell surface glycoprotein CD1b precursor

See identical proteins and their annotated locations for NP_001755.1

Status: REVIEWED

Source sequence(s)

AI336342, BC104217, CD687240

Consensus CDS

CCDS1176.1

UniProtKB/Swiss-Prot

P29016, Q5TDK9, Q5TDL0, Q9UMM2

UniProtKB/TrEMBL

B4E0D3

Related

ENSP00000357150.3, ENST00000368168.4

Conserved Domains (2) summary

cd07698
Location:203 → 295

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

cl08246
Location:19 → 198

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

158285405..158331531 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017002785.3 → XP_016858274.1 T-cell surface glycoprotein CD1b isoform X3
XM_017002784.3 → XP_016858273.1 T-cell surface glycoprotein CD1b isoform X2
XM_017002786.3 → XP_016858275.1 T-cell surface glycoprotein CD1b isoform X4
XM_011510119.4 → XP_011508421.1 T-cell surface glycoprotein CD1b isoform X1

See identical proteins and their annotated locations for XP_011508421.1

UniProtKB/TrEMBL

H7C0I2

Related

ENSP00000395161.1, ENST00000451207.5

Conserved Domains (2) summary

cl08246
Location:19 → 198

MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

cl11960
Location:203 → 257

Ig; Immunoglobulin domain