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Entry version 143 (02 Dec 2020)
Sequence version 3 (23 Jan 2007)
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Protein

ATP synthase subunit d, mitochondrial

Gene

Atp5pd

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Mitochondrial membrane ATP synthase (F1F0 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, F1 - containing the extramembraneous catalytic core, and F0 - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F1 is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F0 domain and the peripheric stalk, which acts as a stator to hold the catalytic alpha3beta3 subcomplex and subunit a/ATP6 static relative to the rotary elements.

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • protein-containing complex binding Source: RGD
  • proton transmembrane transporter activity Source: RGD

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Biological processHydrogen ion transport, Ion transport, Transport

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-RNO-163210, Formation of ATP by chemiosmotic coupling
R-RNO-8949613, Cristae formation

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
ATP synthase subunit d, mitochondrialCurated
Short name:
ATPase subunit d
Alternative name(s):
ATP synthase peripheral stalk subunit dCurated
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:Atp5pdImported
Synonyms:Atp5h, Atp5jd
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiRattus norvegicus (Rat)
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri10116 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaMyomorphaMuroideaMuridaeMurinaeRattus
<p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000002494 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome 10

Organism-specific databases

Rat genome database

More...
RGDi
620083, Atp5pd

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte & Seán O’Donoghue; Source: COMPARTMENTS

Keywords - Cellular componenti

CF(0), Membrane, Mitochondrion, Mitochondrion inner membrane

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/ptm%5Fprocessing%5Fsection">PTM / Processing</a> section indicates that the initiator methionine is cleaved from the mature protein.<p><a href='/help/init_met' target='_top'>More...</a></p>Initiator methionineiRemovedBy similarity
<p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00000716752 – 161ATP synthase subunit d, mitochondrialAdd BLAST160

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'PTM / Processing' section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei2N-acetylalanineBy similarity1
Modified residuei32N6-acetyllysineBy similarity1
Modified residuei48N6-acetyllysineBy similarity1
Modified residuei63N6-acetyllysineBy similarity1
Modified residuei78N6-acetyllysine; alternateBy similarity1
Modified residuei78N6-succinyllysine; alternateBy similarity1
Modified residuei85N6-acetyllysine; alternateBy similarity1
Modified residuei85N6-succinyllysine; alternateBy similarity1
Modified residuei95N6-acetyllysine; alternateBy similarity1
Modified residuei95N6-succinyllysine; alternateBy similarity1
Modified residuei117N6-acetyllysineBy similarity1
Modified residuei144N6-acetyllysine; alternateBy similarity1
Modified residuei144N6-succinyllysine; alternateBy similarity1
Modified residuei149N6-acetyllysine; alternateBy similarity1
Modified residuei149N6-succinyllysine; alternateBy similarity1

Keywords - PTMi

Acetylation

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P31399

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P31399

PRoteomics IDEntifications database

More...
PRIDEi
P31399

2D gel databases

The World-2DPAGE database

More...
World-2DPAGEi
0004:P31399

PTM databases

CarbonylDB database of protein carbonylation sites

More...
CarbonylDBi
P31399

iPTMnet integrated resource for PTMs in systems biology context

More...
iPTMneti
P31399

Comprehensive resource for the study of protein post-translational modifications (PTMs) in human, mouse and rat.

More...
PhosphoSitePlusi
P31399

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSRNOG00000003626, Expressed in heart and 20 other tissues

Genevisible search portal to normalized and curated expression data from Genevestigator

More...
Genevisiblei
P31399, RN

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

F-type ATPases have 2 components, CF1 - the catalytic core - and CF0 - the membrane proton channel. CF0 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.

1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGRID)

More...
BioGRIDi
566012, 3 interactors

CORUM comprehensive resource of mammalian protein complexes

More...
CORUMi
P31399

Protein interaction database and analysis system

More...
IntActi
P31399, 1 interactor

STRING: functional protein association networks

More...
STRINGi
10116.ENSRNOP00000004836

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
P31399

Database of comparative protein structure models

More...
ModBasei
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the ATPase d subunit family.Curated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
KOG3366, Eukaryota

Ensembl GeneTree

More...
GeneTreei
ENSGT00390000003582

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_130600_0_0_1

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P31399

Identification of Orthologs from Complete Genome Data

More...
OMAi
PYPQDKV

Database of Orthologous Groups

More...
OrthoDBi
1299717at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P31399

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.20.58.880, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR008689, ATP_synth_F0_dsu_mt
IPR036228, ATP_synth_F0_dsu_sf_mt

The PANTHER Classification System

More...
PANTHERi
PTHR12700, PTHR12700, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF05873, Mt_ATP-synt_D, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF005514, ATPase_F0_D_mt, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF161065, SSF161065, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is in its mature form or if it represents the precursor.<p><a href='/help/sequence_processing' target='_top'>More...</a></p>Sequence processingi: The displayed sequence is further processed into a mature form.

P31399-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MAGRKLALKT IDWVSFVEIM PQNQKAIGNA LKSWNETFHT RLASLSEKPP
60 70 80 90 100
AIDWAYYRAN VDKPGLVDDF KNKYNALKIP VPEDKYTALV DAEEKEDVKN
110 120 130 140 150
CAQFVTGSQA RVREYEKQLE KIKNMIPFDQ MTIDDLNEVF PETKLDKRKY
160
PYWPHQPIEN L
Length:161
Mass (Da):18,763
Last modified:January 23, 2007 - v3
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i285F075DE5641261
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Sequence' section reports difference(s) between the canonical sequence (displayed by default in the entry) and the different sequence submissions merged in the entry. These various submissions may originate from different sequencing projects, different types of experiments, or different biological samples. Sequence conflicts are usually of unknown origin.<p><a href='/help/conflict' target='_top'>More...</a></p>Sequence conflicti79I → D in BAA00911 (PubMed:1531750).Curated1
Sequence conflicti141P → L in BAA00911 (PubMed:1531750).Curated1

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
D10021 mRNA Translation: BAA00911.1
D13120 mRNA Translation: BAA02422.1
BC059139 mRNA Translation: AAH59139.1
BC078846 mRNA Translation: AAH78846.1

Protein sequence database of the Protein Information Resource

More...
PIRi
JS0739

NCBI Reference Sequences

More...
RefSeqi
NP_062256.1, NM_019383.2

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSRNOT00000004836; ENSRNOP00000004836; ENSRNOG00000003626

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
641434

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
rno:641434

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
D10021 mRNA Translation: BAA00911.1
D13120 mRNA Translation: BAA02422.1
BC059139 mRNA Translation: AAH59139.1
BC078846 mRNA Translation: AAH78846.1
PIRiJS0739
RefSeqiNP_062256.1, NM_019383.2

3D structure databases

SMRiP31399
ModBaseiSearch...

Protein-protein interaction databases

BioGRIDi566012, 3 interactors
CORUMiP31399
IntActiP31399, 1 interactor
STRINGi10116.ENSRNOP00000004836

PTM databases

CarbonylDBiP31399
iPTMnetiP31399
PhosphoSitePlusiP31399

2D gel databases

World-2DPAGEi0004:P31399

Proteomic databases

jPOSTiP31399
PaxDbiP31399
PRIDEiP31399

Genome annotation databases

EnsembliENSRNOT00000004836; ENSRNOP00000004836; ENSRNOG00000003626
GeneIDi641434
KEGGirno:641434

Organism-specific databases

Comparative Toxicogenomics Database

More...
CTDi
10476
RGDi620083, Atp5pd

Phylogenomic databases

eggNOGiKOG3366, Eukaryota
GeneTreeiENSGT00390000003582
HOGENOMiCLU_130600_0_0_1
InParanoidiP31399
OMAiPYPQDKV
OrthoDBi1299717at2759
PhylomeDBiP31399

Enzyme and pathway databases

ReactomeiR-RNO-163210, Formation of ATP by chemiosmotic coupling
R-RNO-8949613, Cristae formation

Miscellaneous databases

Protein Ontology

More...
PROi
PR:P31399

Gene expression databases

BgeeiENSRNOG00000003626, Expressed in heart and 20 other tissues
GenevisibleiP31399, RN

Family and domain databases

Gene3Di1.20.58.880, 1 hit
InterProiView protein in InterPro
IPR008689, ATP_synth_F0_dsu_mt
IPR036228, ATP_synth_F0_dsu_sf_mt
PANTHERiPTHR12700, PTHR12700, 1 hit
PfamiView protein in Pfam
PF05873, Mt_ATP-synt_D, 1 hit
PIRSFiPIRSF005514, ATPase_F0_D_mt, 1 hit
SUPFAMiSSF161065, SSF161065, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiATP5H_RAT
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P31399
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: January 23, 2007
Last modified: December 2, 2020
This is version 143 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
UniProt is an ELIXIR core data resource
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