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ATP6V0D1 ATPase H+ transporting V0 subunit d1 [ Homo sapiens (human) ]

Gene ID: 9114, updated on 3-May-2020

Summary

Official Symbol
ATP6V0D1provided by HGNC
Official Full Name
ATPase H+ transporting V0 subunit d1provided by HGNC
Primary source
HGNC:HGNC:13724
See related
Ensembl:ENSG00000159720 MIM:607028
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
P39; VATX; VMA6; ATP6D; ATP6DV; VPATPD
Summary
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c'', and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This encoded protein is known as the D subunit and is found ubiquitously. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 53.8), thyroid (RPKM 41.0) and 25 other tissues See more
Orthologs

Genomic context

See ATP6V0D1 in Genome Data Viewer
Location:
16q22.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (67438019..67481157, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67471917..67515089, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type containing 1 Neighboring gene hydroxysteroid 11-beta dehydrogenase 2 Neighboring gene uncharacterized LOC101927837 Neighboring gene agouti related neuropeptide Neighboring gene uncharacterized LOC100505942 Neighboring gene RHO family interacting cell polarization regulator 1

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ43534

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
proton-exporting ATPase activity, phosphorylative mechanism IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proton-transporting ATPase activity, rotational mechanism IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
IRE1-mediated unfolded protein response TAS
Traceable Author Statement
more info
 
brain development IEA
Inferred from Electronic Annotation
more info
 
cellular iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to increased oxygen levels IMP
Inferred from Mutant Phenotype
more info
PubMed 
cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
insulin receptor signaling pathway TAS
Traceable Author Statement
more info
 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
phagosome acidification TAS
Traceable Author Statement
more info
 
proton transmembrane transport NAS
Non-traceable Author Statement
more info
PubMed 
regulation of macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
transferrin transport TAS
Traceable Author Statement
more info
 
vacuolar acidification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vacuolar transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
axon terminus IEA
Inferred from Electronic Annotation
more info
 
cell IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
PubMed 
early endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
lysosomal membrane HDA PubMed 
lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
phagocytic vesicle membrane TAS
Traceable Author Statement
more info
 
plasma membrane proton-transporting V-type ATPase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
proton-transporting V-type ATPase, V0 domain IEA
Inferred from Electronic Annotation
more info
 
synaptic vesicle IEA
Inferred from Electronic Annotation
more info
 
vacuolar proton-transporting V-type ATPase complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vacuolar proton-transporting V-type ATPase complex IDA
Inferred from Direct Assay
more info
PubMed 
vacuolar proton-transporting V-type ATPase complex NAS
Non-traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
V-type proton ATPase subunit d 1
Names
32 kDa accessory protein
ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D
ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1
H(+)-transporting two-sector ATPase, subunit D
V-ATPase 40 KDa accessory protein
V-ATPase AC39 subunit
V-ATPase subunit d 1
V-ATPase, subunit D
vacuolar proton pump subunit d 1
NP_004682.2
XP_011521746.1
XP_011521747.1
XP_011521748.1

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.

Genomic

  1. NG_011482.1 RefSeqGene

    Range
    5030..48168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004691.5NP_004682.2  V-type proton ATPase subunit d 1

    See identical proteins and their annotated locations for NP_004682.2

    Status: REVIEWED

    Source sequence(s)
    BC008861, BM677562
    Consensus CDS
    CCDS10838.1
    UniProtKB/Swiss-Prot
    P61421
    Related
    ENSP00000290949.3, ENST00000290949.8
    Conserved Domains (1) summary
    pfam01992
    Location:16344
    vATP-synt_AC39; ATP synthase (C/AC39) subunit

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    67438019..67481157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011523444.1XP_011521746.1  V-type proton ATPase subunit d 1 isoform X1

    See identical proteins and their annotated locations for XP_011521746.1

    UniProtKB/TrEMBL
    R4GN72
    Conserved Domains (1) summary
    pfam01992
    Location:1267
    vATP-synt_AC39; ATP synthase (C/AC39) subunit
  2. XM_011523445.1XP_011521747.1  V-type proton ATPase subunit d 1 isoform X1

    See identical proteins and their annotated locations for XP_011521747.1

    UniProtKB/TrEMBL
    R4GN72
    Conserved Domains (1) summary
    pfam01992
    Location:1267
    vATP-synt_AC39; ATP synthase (C/AC39) subunit
  3. XM_011523446.1XP_011521748.1  V-type proton ATPase subunit d 1 isoform X1

    See identical proteins and their annotated locations for XP_011521748.1

    UniProtKB/TrEMBL
    R4GN72
    Related
    ENSP00000473515.1, ENST00000602876.5
    Conserved Domains (1) summary
    pfam01992
    Location:1267
    vATP-synt_AC39; ATP synthase (C/AC39) subunit
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