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ATP5PD ATP synthase peripheral stalk subunit d [ Homo sapiens (human) ]

Gene ID: 10476, updated on 2-Nov-2024

Summary

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Official Symbol
ATP5PDprovided by HGNC
Official Full Name
ATP synthase peripheral stalk subunit dprovided by HGNC
Primary source
HGNC:HGNC:845
See related
Ensembl:ENSG00000167863 MIM:618121; AllianceGenome:HGNC:845
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
ATPQ; APT5H; ATP5H
Summary
Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. It is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, which comprises the proton channel. The F1 complex consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled in a ratio of 3 alpha, 3 beta, and a single representative of the other 3. The Fo seems to have nine subunits (a, b, c, d, e, f, g, F6 and 8). This gene encodes the d subunit of the Fo complex. Alternatively spliced transcript variants encoding different isoforms have been identified for this gene. In addition, three pseudogenes are located on chromosomes 9, 12 and 15. [provided by RefSeq, Jun 2010]
Expression
Ubiquitous expression in heart (RPKM 220.3), kidney (RPKM 160.7) and 25 other tissues See more
Orthologs
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Genomic context

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See ATP5PD in Genome Data Viewer
Location:
17q25.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (75038863..75046969, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (75930610..75938401, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (73034958..73043064, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73029803-73030784 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12730 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8952 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:73031872-73032031 Neighboring gene tRNA-Arg (anticodon CCT) 2-1 Neighboring gene tRNA-Arg (anticodon TCG) 3-1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73037362-73037932 Neighboring gene potassium channel tetramerization domain containing 2 Neighboring gene RNA, 7SL, cytoplasmic 573, pseudogene Neighboring gene Sharpr-MPRA regulatory region 3986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12732 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:73074528-73075727 Neighboring gene tripartite motif containing 80, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8954 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089299-73089872 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:73089873-73090445 Neighboring gene solute carrier family 16 member 5 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73100784-73101284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:73101285-73101785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8955 Neighboring gene armadillo repeat containing 7

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 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. Mitochondrial reprogramming via ATP5H loss promotes multimodal cancer therapy resistance. Song KH, et al. J Clin Invest, 2018 Aug 31. PMID 30124467, Free PMC Article
  2. ATP5H/KCTD2 locus is associated with Alzheimer's disease risk. Boada M, et al. Mol Psychiatry, 2014 Jun. PMID 23857120, Free PMC Article
  3. Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males. Katz Shroitman N, et al. J Psychiatr Res, 2023 Feb. PMID 36640659
  4. The complete amino acid sequence of subunit d of rat liver mitochondrial H(+)-ATP synthase. Higuti T, et al. J Biochem, 1993 Nov. PMID 7509337
  5. Systems biology approach to late-onset Alzheimer's disease genome-wide association study identifies novel candidate genes validated using brain expression data and Caenorhabditis elegans experiments. Mukherjee S, et al. Alzheimers Dement, 2017 Oct. PMID 28242297, Free PMC Article

See all (109) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males.
    Title: Meta-analysis of brain samples of individuals with schizophrenia detects down-regulation of multiple ATP synthase encoding genes in both females and males.
  2. ATP5H loss in the tumor is strongly linked to failure of therapy, disease progression, and poor survival in patients with cancer.
    Title: Mitochondrial reprogramming via ATP5H loss promotes multimodal cancer therapy resistance.
  3. The Network analyses identified ATP5H expression in temporal cortex in patient with late-onset Alzheimer's disease.
    Title: Systems biology approach to late-onset Alzheimer's disease genome-wide association study identifies novel candidate genes validated using brain expression data and Caenorhabditis elegans experiments.
  4. By merging results of a meta-GWAS, results in the CHARGE consortium data sets and an in vivo genotyping comprising 4501 individuals, detected a novel locus ATP5H/KCTD2 associated with Alzheimer's disease risk
    Title: ATP5H/KCTD2 locus is associated with Alzheimer's disease risk.
  5. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  6. This protein has been found differentially expressed in the dorsolateral prefrontal cortex from patients with schizophrenia.
    Title: Proteomic analysis of dorsolateral prefrontal cortex indicates the involvement of cytoskeleton, oligodendrocyte, energy metabolism and new potential markers in schizophrenia.
Submit: New GeneRIF Correction

Phenotypes

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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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Protein interactions

Protein Gene Interaction Pubs
Vpu vpu HIV-1 Vpu is identified to have a physical interaction with ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d (ATP5H) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses 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 
contributes_to proton-transporting ATP synthase activity, rotational mechanism IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to proton-transporting ATP synthase activity, rotational mechanism IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in proton motive force-driven ATP synthesis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in proton motive force-driven ATP synthesis NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in proton motive force-driven mitochondrial ATP synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in mitochondrial inner membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrial inner membrane NAS
Non-traceable Author Statement
more info
 PubMed 
located_in mitochondrial inner membrane TAS
Traceable Author Statement
more info
  
located_in mitochondrion HDA PubMed 
located_in mitochondrion HTP PubMed 
located_in mitochondrion IC
Inferred by Curator
more info
 PubMed 
located_in mitochondrion IDA
Inferred from Direct Assay
more info
  
part_of proton-transporting ATP synthase complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
ATP synthase subunit d, mitochondrial
Names
ATP synthase D chain, mitochondrial
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d
ATP synthase, H+ transporting, mitochondrial F1F0, subunit d
ATP synthase, H+ transporting, mitochondrial Fo complex subunit D
ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d
ATPase subunit d
My032 protein
NP_001003785.1
NP_006347.1

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_001003785.2 → NP_001003785.1  ATP synthase subunit d, mitochondrial isoform b

    See identical proteins and their annotated locations for NP_001003785.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame segment of the coding region, compared to variant 1. It encodes a shorter isoform (b), that is missing an internal segment compared to isoform a.
    Source sequence(s)
    AA608885, BC032245
    Consensus CDS
    CCDS32727.1
    UniProtKB/Swiss-Prot
    O75947
    Related
    ENSP00000344230.4, ENST00000344546.8
    Conserved Domains (1) summary
    pfam05873
    Location:3 → 131
    Mt_ATP-synt_D; ATP synthase D chain, mitochondrial (ATP5H)

  2. NM_006356.3 → NP_006347.1  ATP synthase subunit d, mitochondrial isoform a

    See identical proteins and their annotated locations for NP_006347.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript, and it encodes the longer isoform a.
    Source sequence(s)
    AA608885, BC029392, BC032245, BC038092
    Consensus CDS
    CCDS11712.1
    UniProtKB/Swiss-Prot
    B2R5L6, O75947, Q9H3J4
    Related
    ENSP00000301587.4, ENST00000301587.9
    Conserved Domains (1) summary
    pfam05873
    Location:3 → 155
    Mt_ATP-synt_D; ATP synthase D chain, mitochondrial (ATP5H)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    75038863..75046969 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    75930610..75938401 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75947.3 GenPept UniProtKB/Swiss-Prot:O75947

Gene LinkOut

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