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ATP6V0B ATPase H+ transporting V0 subunit b [ Homo sapiens (human) ]

Gene ID: 533, updated on 11-Apr-2024

Summary

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Official Symbol
ATP6V0Bprovided by HGNC
Official Full Name
ATPase H+ transporting V0 subunit bprovided by HGNC
Primary source
HGNC:HGNC:861
See related
Ensembl:ENSG00000117410 MIM:603717; AllianceGenome:HGNC:861
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
ATP6F; HATPL; VMA16
Summary
This gene encodes a portion of the V0 domain of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Activity of this enzyme is necessary for such varied processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Ubiquitous expression in bone marrow (RPKM 52.4), kidney (RPKM 31.0) and 25 other tissues See more
Orthologs
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Genomic context

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See ATP6V0B in Genome Data Viewer
Location:
1p34.1
Exon count:
9
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (43974960..43978295)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (43846040..43849375)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (44440632..44443967)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 796 Neighboring gene importin 13 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:44426574-44427773 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 928 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44436478-44437024 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:44437355-44438554 Neighboring gene uncharacterized LOC124904167 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44439785-44440618 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44440619-44441451 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44443584-44444175 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:44444176-44444766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:44444767-44445358 Neighboring gene diphthamide biosynthesis 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:44447723-44448312 Neighboring gene beta-1,4-galactosyltransferase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 801 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 802 Neighboring gene Sharpr-MPRA regulatory region 11322 Neighboring gene coiled-coil domain containing 24 Neighboring gene solute carrier family 6 member 9

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Plasmalemmal V-H(+)-ATPases regulate intracellular pH in human lung microvascular endothelial cells. Rojas JD, et al. Biochem Biophys Res Commun, 2004 Aug 6. PMID 15249206
  2. Identification and characterization of the gene encoding a second proteolipid subunit of human vacuolar H(+)-ATPase (ATP6F). Nishigori H, et al. Genomics, 1998 Jun 1. PMID 9653649
  3. Structural and functional characterization of two human V-ATPase subunit gene promoters. Izumi H, et al. Biochim Biophys Acta, 2003 Jul 28. PMID 12890556
  4. Physical interaction between aldolase and vacuolar H+-ATPase is essential for the assembly and activity of the proton pump. Lu M, et al. J Biol Chem, 2007 Aug 24. PMID 17576770
  5. Structure and Roles of V-type ATPases. Vasanthakumar T, et al. Trends Biochem Sci, 2020 Apr. PMID 32001091

See all (35) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. there is an important role for physical association between aldolase and the A, B and E subunits of V-ATPase in the regulation of the proton pump
    Title: Physical interaction between aldolase and vacuolar H+-ATPase is essential for the assembly and activity of the proton pump.
  2. These studies show a Na(+)- and HCO(3)(-)-independent pH(cyt) regulatory mechanism in HLMVE cells that is mediated by pmV-ATPases.
    Title: Plasmalemmal V-H(+)-ATPases regulate intracellular pH in human lung microvascular endothelial cells.
  3. proximal promoter region contains cis-acting elements required for expression in cancer cells
    Title: Structural and functional characterization of two human V-ATPase subunit gene promoters.
Submit: New GeneRIF Correction

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)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b (ATP6V0B) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables proton-transporting ATPase activity, rotational mechanism IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in Golgi lumen acidification NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in endosomal lumen acidification NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in intracellular pH reduction NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in lysosomal lumen acidification NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in proton transmembrane transport NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in vacuolar acidification NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in clathrin-coated vesicle membrane IEA
Inferred from Electronic Annotation
more info
  
located_in endosome membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in endosome membrane TAS
Traceable Author Statement
more info
  
located_in lysosomal membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
  
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in phagocytic vesicle membrane TAS
Traceable Author Statement
more info
  
located_in plasma membrane NAS
Non-traceable Author Statement
more info
 PubMed 
part_of proton-transporting V-type ATPase complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of transmembrane transporter complex IEA
Inferred from Electronic Annotation
more info
  
part_of vacuolar proton-transporting V-type ATPase, V0 domain ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
V-type proton ATPase 21 kDa proteolipid subunit c''
Names
ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b
ATPase, H+ transporting, lysosomal, 21-KD, V0 subunit C-prime, prime
ATPase, H+ transporting, lysosomal, subunit F
H(+)-transporting two-sector ATPase, subunit F
V-ATPase 21 kDa proteolipid subunit
V-ATPase 21 kDa proteolipid subunit c''
V-ATPase subunit b
V-ATPase subunit c''
V-type proton ATPase 21 kDa proteolipid subunit
vacuolar ATP synthase 21 kDa proteolipid subunit
vacuolar proton pump 21 kDa proteolipid subunit
vacuolar proton pump 21 kDa proteolipid subunit c''
NP_001034546.1
NP_001281262.1
NP_004038.1
XP_047278606.1
XP_054193068.1

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)

  1. NM_001039457.3 → NP_001034546.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 2

    See identical proteins and their annotated locations for NP_001034546.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame in the 5' coding region and uses a downstream start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI439545, BG475609, D89052
    Consensus CDS
    CCDS41315.1
    UniProtKB/Swiss-Prot
    Q99437
    Related
    ENSP00000236067.4, ENST00000236067.8
    Conserved Domains (2) summary
    cd18177
    Location:2 → 64
    ATP-synt_Vo_c_ATP6F_rpt1; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins
    cd18178
    Location:86 → 150
    ATP-synt_Vo_c_ATP6F_rpt2; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins

  2. NM_001294333.2 → NP_001281262.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 3

    See identical proteins and their annotated locations for NP_001281262.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate segment in the 3' region, which results in a frameshift, compared to variant 1. The encoded isoform (3) has a longer and distinct C-terminus, compared to variant 1.
    Source sequence(s)
    AL357079
    Consensus CDS
    CCDS72772.1
    UniProtKB/TrEMBL
    E9PNL3
    Related
    ENSP00000434729.1, ENST00000532642.5
    Conserved Domains (2) summary
    PRK08344
    Location:48 → 199
    PRK08344; V-type ATP synthase subunit K; Validated
    pfam00137
    Location:136 → 196
    ATP-synt_C; ATP synthase subunit C

  3. NM_004047.5 → NP_004038.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform 1

    See identical proteins and their annotated locations for NP_004038.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform 1.
    Source sequence(s)
    AI439545, D89052
    Consensus CDS
    CCDS505.1
    UniProtKB/Swiss-Prot
    D3DPY5, Q6IB32, Q99437
    UniProtKB/TrEMBL
    E9PNU0
    Related
    ENSP00000431605.1, ENST00000472174.7
    Conserved Domains (2) summary
    cd18177
    Location:49 → 111
    ATP-synt_Vo_c_ATP6F_rpt1; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins
    cd18178
    Location:133 → 197
    ATP-synt_Vo_c_ATP6F_rpt2; V-type proton ATPase 21 kDa proteolipid subunit (ATP6F/ATP6V0B) and similar proteins

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

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    43974960..43978295
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047422650.1 → XP_047278606.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1

    Related
    ENSP00000434094.1, ENST00000498664.1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    43846040..43849375
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337093.1 → XP_054193068.1  V-type proton ATPase 21 kDa proteolipid subunit c'' isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q99437.1 GenPept UniProtKB/Swiss-Prot:Q99437

Gene LinkOut

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