ATP5PD Gene (Protein Coding)

ATP Synthase Peripheral Stalk Subunit D

GC17M075039
GIFtS:
32
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, ... See more...

Aliases for ATP5PD Gene

Aliases for ATP5PD Gene

  • ATP Synthase Peripheral Stalk Subunit D 2 3 4 5
  • ATP Synthase, H+ Transporting, Mitochondrial F0 Complex, Subunit D 2 3
  • ATP Synthase, H+ Transporting, Mitochondrial Fo Complex, Subunit D 2 3
  • ATP Synthase, H+ Transporting, Mitochondrial Fo Complex Subunit D 2 3
  • ATP Synthase Subunit D, Mitochondrial 3 4
  • ATPase Subunit D 3 4
  • ATP5H 3 4
  • ATPQ 2 3
  • ATP Synthase, H+ Transporting, Mitochondrial F1F0, Subunit D 3
  • ATP Synthase D Chain, Mitochondrial 3
  • My032 Protein 3
  • ATP5PD 5
  • ATP5JD 2
  • APT5H 3

External Ids for ATP5PD Gene

Previous HGNC Symbols for ATP5PD Gene

  • ATP5H

Summaries for ATP5PD Gene

Entrez Gene Summary for ATP5PD Gene

  • 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]

GeneCards Summary for ATP5PD Gene

ATP5PD (ATP Synthase Peripheral Stalk Subunit D) is a Protein Coding gene. Diseases associated with ATP5PD include Dystonia 11, Myoclonic and Amyotrophic Lateral Sclerosis 1. Among its related pathways are Pathways of neurodegeneration - multiple diseases and purine nucleotides de novo biosynthesis.

UniProtKB/Swiss-Prot Summary for ATP5PD Gene

  • Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements.

Gene Wiki entry for ATP5PD Gene

Additional gene information for ATP5PD Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ATP5PD Gene

Genomics for ATP5PD Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for ATP5PD Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ATP5PD on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ATP5PD

Genomic Locations for ATP5PD Gene

Latest Assembly
chr17:75,038,863-75,046,985
(GRCh38/hg38)
Size:
8,123 bases
Orientation:
Minus strand

Previous Assembly
chr17:73,034,958-73,043,064
(GRCh37/hg19 by Entrez Gene)
Size:
8,107 bases
Orientation:
Minus strand

chr17:73,034,958-73,043,080
(GRCh37/hg19 by Ensembl)
Size:
8,123 bases
Orientation:
Minus strand

Genomic View for ATP5PD Gene

Genes around ATP5PD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ATP5PD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ATP5PD Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for ATP5PD Gene

Proteins for ATP5PD Gene

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  • Protein details for ATP5PD Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O75947-ATP5H_HUMAN
    Recommended name:
    ATP synthase subunit d, mitochondrial
    Protein Accession:
    O75947
    Secondary Accessions:
    • B2R5L6
    • Q9H3J4

    Protein attributes for ATP5PD Gene

    Size:
    161 amino acids
    Molecular mass:
    18491 Da
    Quaternary structure:
    • F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(0) seems to have nine subunits: a, b, c, d, e, f, g, F6 and 8 (or A6L). Component of an ATP synthase complex composed of ATP5PB, ATP5MC1, ATP5F1E, ATP5PD, ATP5ME, ATP5PF, ATP5MF, MT-ATP6, MT-ATP8, ATP5F1A, ATP5F1B, ATP5F1D, ATP5F1C, ATP5PO, ATP5MG, ATP5MD and ATP5MPL (By similarity).

    Alternative splice isoforms for ATP5PD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ATP5PD Gene

Post-translational modifications for ATP5PD Gene

  • Ubiquitination at Lys32
  • Modification sites at PhosphoSitePlus

Other Protein References for ATP5PD Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for ATP5PD

No data available for DME Specific Peptides for ATP5PD Gene

Domains & Families for ATP5PD Gene

Gene Families for ATP5PD Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ATP5PD Gene

InterPro:
Blocks:
  • ATP synthase D chain, mitochondrial

Suggested Antigen Peptide Sequences for ATP5PD Gene

GenScript: Design optimal peptide antigens:
  • ATP5H protein (A0PJH2_HUMAN)
  • ATP synthase subunit d, mitochondrial (ATP5H_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O75947

UniProtKB/Swiss-Prot:

ATP5H_HUMAN :
  • Belongs to the ATPase d subunit family.
Family:
  • Belongs to the ATPase d subunit family.
genes like me logo Genes that share domains with ATP5PD: view

Function for ATP5PD Gene

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  6. Cell Lines for research

Molecular function for ATP5PD Gene

UniProtKB/Swiss-Prot Function:
Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha(3)beta(3) subcomplex and subunit a/ATP6 static relative to the rotary elements.

Phenotypes From GWAS Catalog for ATP5PD Gene

Gene Ontology (GO) - Molecular Function for ATP5PD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 19688755
GO:0015078 proton transmembrane transporter activity IEA --
GO:0044877 protein-containing complex binding IEA --
GO:0046933 contributes_to proton-transporting ATP synthase activity, rotational mechanism IDA 12110673
genes like me logo Genes that share ontologies with ATP5PD: view
genes like me logo Genes that share phenotypes with ATP5PD: view

miRNA for ATP5PD Gene

miRTarBase miRNAs that target ATP5PD

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ATP5PD Gene

Localization for ATP5PD Gene

Subcellular locations from UniProtKB/Swiss-Prot for ATP5PD Gene

Mitochondrion. Mitochondrion inner membrane.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ATP5PD gene
Compartment Confidence
mitochondrion 5
cytosol 4
nucleus 3
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Mitochondria (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for ATP5PD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000274 mitochondrial proton-transporting ATP synthase, stator stalk IBA 21873635
GO:0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) IEA --
GO:0005739 mitochondrion IEA,IDA --
GO:0005743 mitochondrial inner membrane IEA,TAS --
GO:0005753 mitochondrial proton-transporting ATP synthase complex IDA 12110673
genes like me logo Genes that share ontologies with ATP5PD: view

Pathways & Interactions for ATP5PD Gene

genes like me logo Genes that share pathways with ATP5PD: view

Gene Ontology (GO) - Biological Process for ATP5PD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006754 ATP biosynthetic process TAS --
GO:0006811 ion transport IEA --
GO:0015986 ATP synthesis coupled proton transport IEA,IBA 21873635
GO:0042407 cristae formation TAS --
GO:0042776 mitochondrial ATP synthesis coupled proton transport TAS --
genes like me logo Genes that share ontologies with ATP5PD: view

No data available for SIGNOR curated interactions for ATP5PD Gene

Drugs & Compounds for ATP5PD Gene

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(3) Drugs for ATP5PD Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Water Approved Pharma 0
Phosphate Experimental Pharma 0
ATP Investigational Nutra 0

(1) Additional Compounds for ATP5PD Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
 58-64-0
genes like me logo Genes that share compounds with ATP5PD: view

Transcripts for ATP5PD Gene

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mRNA/cDNA for ATP5PD Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Alternative Splicing Database (ASD) splice patterns (SP) for ATP5PD Gene

No ASD Table

Relevant External Links for ATP5PD Gene

GeneLoc Exon Structure for
ATP5PD

Expression for ATP5PD Gene

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  1. Primer products for research

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ATP5PD

Evidence on tissue expression from TISSUES for ATP5PD Gene

  • Nervous system(4.7)
  • Liver(4.7)
  • Blood(4.5)
  • Pancreas(4.4)
  • Heart(3.8)
  • Muscle(3.6)
  • Kidney(3.4)
  • Intestine(3)
  • Spleen(2.8)
  • Skin(2.7)
  • Stomach(2.7)
  • Lung(2.7)
  • Thyroid gland(2.5)
  • Adrenal gland(2.1)
No Expression Related Data Available

Primer products for research

No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for ATP5PD Gene

Orthologs for ATP5PD Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for ATP5PD Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia ATP5H 29 30
  • 100 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia -- 30
  • 91 (a)
 OneToMany
-- 30
  • 91 (a)
 OneToMany
-- 30
  • 91 (a)
 OneToMany
-- 30
  • 91 (a)
 OneToMany
LOC102154055 29
  • 90.48 (n)
-- 30
  • 90 (a)
 OneToMany
-- 30
  • 90 (a)
 OneToMany
-- 30
  • 89 (a)
 OneToMany
-- 30
  • 89 (a)
 OneToMany
-- 30
  • 89 (a)
 OneToMany
-- 30
  • 89 (a)
 OneToMany
-- 30
  • 89 (a)
 OneToMany
-- 30
  • 88 (a)
 OneToMany
-- 30
  • 88 (a)
 OneToMany
-- 30
  • 88 (a)
 OneToMany
-- 30
  • 88 (a)
 OneToMany
-- 30
  • 87 (a)
 OneToMany
-- 30
  • 87 (a)
 OneToMany
-- 30
  • 87 (a)
 OneToMany
-- 30
  • 87 (a)
 OneToMany
-- 30
  • 86 (a)
 OneToMany
-- 30
  • 86 (a)
 OneToMany
-- 30
  • 85 (a)
 OneToMany
-- 30
  • 85 (a)
 OneToMany
-- 30
  • 82 (a)
 OneToMany
-- 30
  • 82 (a)
 OneToMany
-- 30
  • 82 (a)
 OneToMany
-- 30
  • 80 (a)
 OneToMany
-- 30
  • 77 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia ATP5H 29 30
  • 89.03 (n)
 OneToMany
-- 30
  • 80 (a)
 OneToMany
Mouse
(Mus musculus)
 Mammalia Gm10250 30
  • 81 (a)
 OneToMany
Atp5h 29 16 30
  • 80.54 (n)
 OneToMany
Gm4953 30
  • 75 (a)
 OneToMany
Rat
(Rattus norvegicus)
 Mammalia Atp5h 29
  • 78.88 (n)
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 30
  • 78 (a)
 OneToMany
-- 30
  • 67 (a)
 OneToMany
Oppossum
(Monodelphis domestica)
 Mammalia ATP5H 30
  • 75 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves ATP5H 29 30
  • 68.53 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia ATP5H 30
  • 58 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia atp5h 29
  • 61.9 (n)
Str.1257 29
African clawed frog
(Xenopus laevis)
 Amphibia Xl.23901 29
Zebrafish
(Danio rerio)
 Actinopterygii atp5h 29 30
  • 65.22 (n)
 OneToOne
zgc73071 29
Rainbow Trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.8409 29
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP011131 29
  • 55.35 (n)
Fruit Fly
(Drosophila melanogaster)
 Insecta ATPsyn-d 29 30
  • 53.21 (n)
 OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes ATP7 32
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.7968 30
  • 29 (a)
 OneToOne
Species where no ortholog for ATP5PD was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for ATP5PD Gene

ENSEMBL:
Gene Tree for ATP5PD (if available)
TreeFam:
Gene Tree for ATP5PD (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ATP5PD: view image
Alliance of Genome Resources:
Additional Orthologs for ATP5PD

Paralogs for ATP5PD Gene

Pseudogenes.org Pseudogenes for ATP5PD Gene

genes like me logo Genes that share paralogs with ATP5PD: view

No data available for Paralogs for ATP5PD Gene

Variants for ATP5PD Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for ATP5PD Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for ATP5PD Gene

Variant ID Type Subtype PubMed ID
esv1720628 CNV deletion 17803354
esv2566082 CNV deletion 19546169
esv2716235 CNV deletion 23290073
esv3554781 CNV deletion 23714750
esv3893044 CNV loss 25118596
nsv112456 CNV deletion 16902084

Variation tolerance for ATP5PD Gene

Residual Variation Intolerance Score: 57.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.22; 4.85% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ATP5PD Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ATP5PD
Leiden Open Variation Database (LOVD)
ATP5PD

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ATP5PD Gene

Disorders for ATP5PD Gene

MalaCards: The human disease database

(2) MalaCards diseases for ATP5PD Gene - From: COP

Disorder Aliases PubMed IDs
dystonia 11, myoclonic
  • dyt11
amyotrophic lateral sclerosis 1
  • als1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for ATP5PD

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with ATP5PD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ATP5PD Gene

Publications for ATP5PD Gene

  1. Cloning and functional analysis of cDNAs with open reading frames for 300 previously undefined genes expressed in CD34+ hematopoietic stem/progenitor cells. (PMID: 11042152) Zhang QH … Chen Z (Genome research 2000) 2 3 4
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. (PMID: 32203420) Müller PM … Rocks O (Nature cell biology 2020) 3
  5. A High-Density Human Mitochondrial Proximity Interaction Network. (PMID: 32877691) Antonicka H … Shoubridge EA (Cell metabolism 2020) 3

ExternalLinks

View latest publications for ATP5PD gene in Mastermind

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