Human Gene ATP5F1D (ENST00000395633.5) from GENCODE V41
  Description: Homo sapiens ATP synthase F1 subunit delta (ATP5F1D), transcript variant 2, mRNA. (from RefSeq NM_001001975)
RefSeq Summary (NM_001001975): This gene encodes a subunit of mitochondrial ATP synthase. Mitochondrial ATP synthase catalyzes ATP synthesis, utilizing an electrochemical gradient of protons across the inner membrane during oxidative phosphorylation. ATP synthase is composed of two linked multi-subunit complexes: the soluble catalytic core, F1, and the membrane-spanning component, Fo, comprising the proton channel. The catalytic portion of mitochondrial ATP synthase consists of 5 different subunits (alpha, beta, gamma, delta, and epsilon) assembled with a stoichiometry of 3 alpha, 3 beta, and a single representative of the other 3. The proton channel consists of three main subunits (a, b, c). This gene encodes the delta subunit of the catalytic core. Alternatively spliced transcript variants encoding the same isoform have been identified. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000395633.5
Gencode Gene: ENSG00000099624.8
Transcript (Including UTRs)
   Position: hg38 chr19:1,241,746-1,244,825 Size: 3,080 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg38 chr19:1,241,851-1,244,437 Size: 2,587 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsRNA-Seq ExpressionMicroarray ExpressionRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Methods
Data last updated at UCSC: 2022-05-14 09:57:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:1,241,746-1,244,825)mRNA (may differ from genome)Protein (168 aa)
Gene SorterGenome BrowserOther Species FASTATable SchemaAlphaFoldBioGPS
EnsemblEntrez GeneExonPrimerGencodeGeneCardsHPRD
LynxMGIneXtProtOMIMPubMedReactome
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: ATPD_HUMAN
DESCRIPTION: RecName: Full=ATP synthase subunit delta, mitochondrial; AltName: Full=F-ATPase delta subunit; Flags: Precursor;
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 turnover 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(1) domain and of the central stalk which is part of the complex rotary element. Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits.
SUBUNIT: F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). 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 ATP5F1, ATP5G1, ATP5E, ATP5H, ATP5I, ATP5J, ATP5J2, MT-ATP6, MT-ATP8, ATP5A1, ATP5B, ATP5D, ATP5C1, ATP5O, ATP5L, USMG5 and MP68 (By similarity).
SUBCELLULAR LOCATION: Mitochondrion. Mitochondrion inner membrane.
SIMILARITY: Belongs to the ATPase epsilon chain family.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 180.73 RPKM in Muscle - Skeletal
Total median expression: 4231.64 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -27.50105-0.262 Picture PostScript Text
3' UTR -20.7092-0.225 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001469 - ATPase_F1-cplx_dsu/esu
IPR020547 - ATPase_F1-cplx_dsu/esu_C
IPR020546 - ATPase_F1-cplx_dsu/esu_N

Pfam Domains:
PF02823 - ATP synthase, Delta/Epsilon chain, beta-sandwich domain

ModBase Predicted Comparative 3D Structure on P30049
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005215 transporter activity
GO:0016887 ATPase activity
GO:0022857 transmembrane transporter activity
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism
GO:0005524 ATP binding
GO:0043531 ADP binding

Biological Process:
GO:0006119 oxidative phosphorylation
GO:0006754 ATP biosynthetic process
GO:0006811 ion transport
GO:0015986 ATP synthesis coupled proton transport
GO:0042407 cristae formation
GO:0042776 mitochondrial ATP synthesis coupled proton transport
GO:0046688 response to copper ion
GO:0099132 ATP hydrolysis coupled cation transmembrane transport

Cellular Component:
GO:0000275 mitochondrial proton-transporting ATP synthase complex, catalytic core F(1)
GO:0005739 mitochondrion
GO:0005743 mitochondrial inner membrane
GO:0005753 mitochondrial proton-transporting ATP synthase complex
GO:0005759 mitochondrial matrix
GO:0016020 membrane
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1)


-  Descriptions from all associated GenBank mRNAs
  BC002389 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone MGC:8347 IMAGE:2819749), complete cds.
BC004426 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone MGC:3724 IMAGE:2819749), complete cds.
BC018817 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone IMAGE:2819750).
LF384661 - JP 2014500723-A/192164: Polycomb-Associated Non-Coding RNAs.
MA620238 - JP 2018138019-A/192164: Polycomb-Associated Non-Coding RNAs.
JD461916 - Sequence 442940 from Patent EP1572962.
JD140217 - Sequence 121241 from Patent EP1572962.
AK094357 - Homo sapiens cDNA FLJ37038 fis, clone BRACE2011646, weakly similar to ATP SYNTHASE DELTA CHAIN, MITOCHONDRIAL PRECURSOR (EC 3.6.1.34).
S87916 - Homo sapiens mitochondrial ATP synthase complex delta-subunit precusor mRNA, complete cds, alternatively spliced; nuclear gene for mitochondrial product.
S87918 - Homo sapiens mitochondrial ATP synthase complex delta-subunit precusor mRNA, complete cds, alternatively spliced; nuclear gene for mitochondrial product.
X63422 - Homo sapiens mRNA for delta-subunit of mitochondrial F1F0 ATP-synthase (clone #1).
X63423 - Home sapiens mRNA for delta-subunit of mitochondrial F1F0 ATP-synthase (clone #5).
BC058927 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone IMAGE:5229155), partial cds.
JD467087 - Sequence 448111 from Patent EP1572962.
BC050458 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone IMAGE:5770003), partial cds.
LF323082 - JP 2014500723-A/130585: Polycomb-Associated Non-Coding RNAs.
MA558659 - JP 2018138019-A/130585: Polycomb-Associated Non-Coding RNAs.
KJ890735 - Synthetic construct Homo sapiens clone ccsbBroadEn_00129 ATP5D gene, encodes complete protein.
BC018079 - Homo sapiens ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit, mRNA (cDNA clone MGC:26808 IMAGE:4798666), complete cds.
CR542218 - Homo sapiens full open reading frame cDNA clone RZPDo834C0725D for gene ATP5D, ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit; complete cds, incl. stopcodon.
LF323083 - JP 2014500723-A/130586: Polycomb-Associated Non-Coding RNAs.
MA558660 - JP 2018138019-A/130586: Polycomb-Associated Non-Coding RNAs.
LF323085 - JP 2014500723-A/130588: Polycomb-Associated Non-Coding RNAs.
MA558662 - JP 2018138019-A/130588: Polycomb-Associated Non-Coding RNAs.
LF323087 - JP 2014500723-A/130590: Polycomb-Associated Non-Coding RNAs.
MA558664 - JP 2018138019-A/130590: Polycomb-Associated Non-Coding RNAs.
JD381277 - Sequence 362301 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00190 - Oxidative phosphorylation
hsa01100 - Metabolic pathways
hsa05010 - Alzheimer's disease
hsa05012 - Parkinson's disease
hsa05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein P30049 (Reactome details) participates in the following event(s):

R-HSA-164840 ADP and Pi bind to ATPase
R-HSA-8949580 F1Fo ATP synthase dimerizes
R-HSA-164834 Enzyme-bound ATP is released
R-HSA-164832 ATPase synthesizes ATP
R-HSA-163210 Formation of ATP by chemiosmotic coupling
R-HSA-8949613 Cristae formation
R-HSA-163200 Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
R-HSA-1592230 Mitochondrial biogenesis
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-1852241 Organelle biogenesis and maintenance
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ATP5D, ATPD_HUMAN, D6W5Y3, ENST00000395633.1, ENST00000395633.2, ENST00000395633.3, ENST00000395633.4, NM_001001975, P30049, Q6FG90, uc002lrn.1, uc002lrn.2, uc002lrn.3, uc002lrn.4
UCSC ID: ENST00000395633.5
RefSeq Accession: NM_001001975
Protein: P30049 (aka ATPD_HUMAN)
CCDS: CCDS12058.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.