proton-transporting ATP synthase complex

GO:0045259 · Energy complex · Multiprotein complex · Proposed

The rotary motor enzyme that makes ATP from ADP and phosphate using the ion motive force across the membrane. It has two coupled sectors: a membrane-embedded Fo, whose c-ring turns as protons cross it, and a soluble F1 (alpha3beta3gammadeltaepsilon), whose catalytic beta subunits are driven through their conformational cycle by the rotating gamma subunit. [GO:0045259]

Synonyms: F1Fo ATP synthase

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Genes	Stoichiometry	Essential	Role
F1 catalytic head (alpha3beta3)	Protein complex	part of	atpA, atpD	three alpha and three beta subunits, alternating	ESSENTIAL	Carries the three catalytic sites; ATP is made as each beta subunit passes through its conformational cycle. `DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes the alpha3beta3 head and its three catalytic sites. `DOI:10.1042/bst20110773` Walker 2013 reviews the same sector composition, and the variable c-ring stoichiometry across species.
central stalk (gamma, epsilon)	Protein complex	part of	atpG, atpC		ESSENTIAL	Rotates inside the alpha3beta3 head, driving the catalytic cycle; couples Fo rotation to F1. `DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes the central stalk transmitting rotation into the catalytic head.
Fo c-ring	Protein complex	part of	atpE	8-17 c subunits depending on the organism	ESSENTIAL	The rotor: each subunit carries an ion-binding site, and the ring turns as ions pass. `DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 reviews c-ring stoichiometries and their bearing on the H+/ATP ratio. `DOI:10.1042/bst20110773` Walker 2013 reviews the same sector composition, and the variable c-ring stoichiometry across species.
Fo subunit a	Protein	part of	atpB		ESSENTIAL	Provides the two offset half-channels through which ions enter and leave the c-ring. `DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes the two half-channels in subunit a and the ion path across the membrane.
peripheral stalk (b2, delta)	Protein complex	part of	atpF, atpH		ESSENTIAL	Stator: holds the alpha3beta3 head against the torque of the rotating central stalk. `DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes the peripheral stalk as the stator resisting rotation of the head.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

Fo subunit a

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P0AB98`	ATP synthase subunit a	atpB	Escherichia coli K-12 (`NCBITaxon:83333`)	REVIEWED
Role and evidence (1 reference) The single reviewed UniProtKB entry for gene atpB in Escherichia coli K-12, a taxon this record names; other reviewed entries for this symbol exist on sub-strain nodes and this is the one at the taxon the record names. Identifier for the component's declared gene symbol; it is not itself evidence that the protein is part of this structure. `PMID:15919996` Daley DO et al. 2005, ‘Global topology analysis of the Escherichia coli inner membrane proteome.’, Science. ECO:0000269 experimental evidence cited by UniProt for the 'Cell inner membrane' localisation of P0AB98.

Taxonomic distribution

NCBITaxon:2 Bacteria — UNIVERSAL: Lost only in a few lineages with no membrane bioenergetics. [DOI:10.1146/annurev-biochem-013118-110903]
NCBITaxon:2157 Archaea — UNIVERSAL: Archaea use the related A-type ATP synthase, homologous to the V-type ATPase. [DOI:10.1146/annurev-biochem-013118-110903]

Canonical examples

NCBITaxon:83333 Escherichia coli K-12 — The genetic and biochemical reference for the bacterial F1Fo enzyme (atp operon). [DOI:10.1146/annurev-biochem-013118-110903]
NCBITaxon:1423 Bacillus subtilis — Reference Gram-positive enzyme. [DOI:10.1146/annurev-biochem-013118-110903]
NCBITaxon:562 Escherichia coli — Source organism asserted by the experimental PDB:6OQR ATP synthase entry. [DOI:10.1038/s41467-020-16387-2]

Functions

proton motive force-driven ATP synthesis GO:0015986 — Ion flux down the electrochemical gradient turns the rotor, and rotation drives ATP synthesis in F1.
- DOI:10.1146/annurev-biochem-013118-110903 Kuehlbrandt 2019 reviews rotary catalysis and its coupling to the ion motive force.

Physical properties

SUBUNIT_COUNT: 8-17 (c subunits in the Fo rotor ring, organism-dependent) [DOI:10.1146/annurev-biochem-013118-110903]

Mechanism graphs

Ion flow turns the rotor and the rotor drives catalysis (FUNCTION)

Subject	Predicate	Object	Evidence
proton motive force	drives ion flow through	subunit a half-channels	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019: ions cross via the two offset half-channels in subunit a.
subunit a half-channels	turns	c-ring	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes ion binding at the a/c interface driving c-ring rotation.
c-ring	rotates	central stalk	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019: the c-ring and central stalk rotate as one rotor.
central stalk	drives conformational cycling of	alpha3beta3 catalytic head	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 describes the asymmetric gamma subunit imposing the catalytic cycle on the beta subunits.
alpha3beta3 catalytic head	catalyses formation of `RO:0002327`	ATP	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019: ATP is synthesised at the catalytic interfaces of the head.
alpha3beta3 catalytic head	participates in	proton motive force-driven ATP synthesis	`DOI:10.1146/annurev-biochem-013118-110903` Kuehlbrandt 2019 reviews rotary catalysis as the mechanism of ATP synthesis.

Datasets

E. coli ATP Synthase ADP State 1a (PDB:6OQR) · RCSB_PDB · EXPERIMENTAL_STRUCTURE
Organism: NCBITaxon:562 Escherichia coli · Platform: single-particle cryo-electron microscopy
Released experimental electron microscopy structure at 3.1 Å resolution, with 8 protein entities linked to exact UniProt accessions.
RCSB polymer entity links: 6OQR_1 (ATP synthase subunit delta) = UniProtKB:P0ABA4 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/1]; 6OQR_2 (ATP synthase subunit alpha) = UniProtKB:P0ABB0 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/2]; 6OQR_3 (ATP synthase subunit b) = UniProtKB:P0ABA0 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/3]; 6OQR_4 (ATP synthase epsilon chain) = UniProtKB:P0A6E6 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/4]; 6OQR_5 (ATP synthase gamma chain) = UniProtKB:P0ABA6 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/5]; 6OQR_6 (ATP synthase subunit beta) = UniProtKB:P0ABB4 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/6]; 6OQR_7 (ATP synthase subunit c) = UniProtKB:P68699 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/7]; 6OQR_8 (ATP synthase subunit a) = UniProtKB:P0AB98 [https://data.rcsb.org/rest/v1/core/polymer_entity/6OQR/8]. Biological assembly provenance: assembly 1 has 4 RCSB symmetry annotations (Global Symmetry, Local Symmetry, Pseudo Symmetry); alternate stoichiometries intentionally remain unflattened at [https://data.rcsb.org/rest/v1/core/assembly/6OQR/1]. Deposited 2019-04-29T00:00:00.000+00:00; released 2020-06-03T00:00:00.000+00:00; revised 2025-06-04T00:00:00.000+00:00; primary PMID:32457314; associated EMD-20167. PDB archive and API data are CC0 (https://www.rcsb.org/pages/usage-policy). Metadata-only ingest: the RCSB molecular render is not ingested as an image or counted as a micrograph.
- DOI:10.1038/s41467-020-16387-2

Evidence

DOI:10.1146/annurev-biochem-013118-110903 Kuehlbrandt W 2019, 'Structure and Mechanisms of F-Type ATP Synthases', Annual Review of Biochemistry.
DOI:10.1042/bst20110773 Walker JE 2013, 'The ATP synthase: the understood, the uncertain and the unknown', Biochemical Society Transactions — independent review of subunit composition and rotary catalysis.

Curation history

2026-08-31T03:48:12Z claude · CREATED_RECORD — Drafted from the cited review. Every GO term, taxon id and DOI was resolved against OLS, NCBI Taxonomy and Crossref before writing; evidence notes state what the review says, not a reading of primary literature. Not yet human-reviewed.
2026-08-31T03:54:23Z claude · ADD_CORROBORATION — Added Walker 2013 as an independent second source for composition and rotary catalysis (#63).
2026-08-31T06:12:34Z claude · SET_COMPONENT_ROLE — component_role became required (#77) so the constituent/machinery distinction is machine-readable rather than prose. Set per component; ASSOCIATED_MACHINERY only where the protein acts on the already-assembled structure.
2026-09-02T07:19:02Z codex · ADD_CANONICAL_EXAMPLE — Added the publication-backed NCBITaxon:562 source organism for the exact PDB:6OQR ATP synthase canary before dataset ingestion; did not infer a strain from the species-level RCSB source assertion.
2026-09-02T07:21:58Z rcsb_pdb · ADD_STRUCTURAL_DATASET — Added exact RCSB PDB:6OQR experimental-structure metadata; required the record's pre-existing exact NCBI source taxon, retained DOI/PMID, method, resolution and polymer-entity links, and left alternate assembly stoichiometries unflattened at RCSB. No molecular render was ingested.
2026-09-04T01:40:08Z codex · ENHANCE_CAUSAL_GRAPH — Added descriptions to ATP synthase rotary-catalysis edges so every edge states the ion-flow, rotor, or catalytic step it represents.
2026-09-08T07:39:15Z uniprot_genes · SEED_PROTEIN_EXAMPLES — #183: added 1 protein example(s) by resolving each of the component's declared gene symbols to the single reviewed UniProtKB entry for that symbol in a taxon this record names, deduplicated by accession. Symbols resolving to more than one reviewed entry were skipped rather than chosen between.

Source: data/structures/energy_complex/proton_transporting_atp_synthase_complex.yaml