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Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1E, focussed refinement of F1 head and rotor

Source organism: Polytomella sp. Pringsheim 198.80
Biochemical function: proton-transporting ATP synthase activity, rotational mechanism
Biological process: proton motive force-driven ATP synthesis
Cellular component: membrane

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EC 7.1.2.2: H(+)-transporting two-sector ATPase

Reaction catalysed:
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Systematic name:
ATP phosphohydrolase (two-sector, H(+)-transporting)
Alternative Name(s):
  • ATP synthase
  • Bacterial Ca(2+)/Mg(2+) ATPase
  • Chloroplast ATPase
  • Coupling factors (F(o), F(1) and CF(1))
  • F(0)F(1)-ATPase
  • F(1)-ATPase
  • F(o)F(1)-ATPase
  • H(+)-transporting ATP synthase
  • H(+)-transporting ATPase
  • Mitochondrial ATPase

GO terms

Sequence families

Pfam Protein families (Pfam)
PF00137
Domain description: ATP synthase subunit C
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
The deposited structure of PDB entry 6rdv contains 10 copies of Pfam domain PF00137 (ATP synthase subunit C) in V-ATPase proteolipid subunit C-like domain-containing protein. Showing 1 copy in chain A.

PF00006
Domain description: ATP synthase alpha/beta family, nucleotide-binding domain
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
The deposited structure of PDB entry 6rdv contains 3 copies of Pfam domain PF00006 (ATP synthase alpha/beta family, nucleotide-binding domain) in ATP synthase subunit alpha. Showing 1 copy in chain P [auth U].
The deposited structure of PDB entry 6rdv contains 3 copies of Pfam domain PF00006 (ATP synthase alpha/beta family, nucleotide-binding domain) in ATP synthase subunit beta. Showing 1 copy in chain R [auth X].

PF02874
Domain description: ATP synthase alpha/beta family, beta-barrel domain
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
The deposited structure of PDB entry 6rdv contains 3 copies of Pfam domain PF02874 (ATP synthase alpha/beta family, beta-barrel domain) in ATP synthase subunit alpha. Showing 1 copy in chain P [auth U].
The deposited structure of PDB entry 6rdv contains 3 copies of Pfam domain PF02874 (ATP synthase alpha/beta family, beta-barrel domain) in ATP synthase subunit beta. Showing 1 copy in chain R [auth X].

PF22919
Domain description: C-terminal domain of V and A type ATP synthase
Occurring in:
  1. ATP synthase subunit beta

PF00306
Domain description: ATP synthase alpha/beta chain, C terminal domain
Occurring in:
  1. ATP synthase subunit alpha
The deposited structure of PDB entry 6rdv contains 3 copies of Pfam domain PF00306 (ATP synthase alpha/beta chain, C terminal domain) in ATP synthase subunit alpha. Showing 1 copy in chain P [auth U].

PF00231
Domain description: ATP synthase
Occurring in:
  1. ATP synthase subunit gamma, mitochondrial
The deposited structure of PDB entry 6rdv contains 1 copy of Pfam domain PF00231 (ATP synthase) in ATP synthase subunit gamma, mitochondrial. Showing 1 copy in chain N [auth S].

PF02823
Domain description: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
Occurring in:
  1. ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein
The deposited structure of PDB entry 6rdv contains 1 copy of Pfam domain PF02823 (ATP synthase, Delta/Epsilon chain, beta-sandwich domain) in ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein. Showing 1 copy in chain M [auth R].

PF04627
Domain description: Mitochondrial ATP synthase epsilon chain
Occurring in:
  1. epsilon: Polytomella F-ATP synthase epsilon subunit
The deposited structure of PDB entry 6rdv contains 1 copy of Pfam domain PF04627 (Mitochondrial ATP synthase epsilon chain) in epsilon: Polytomella F-ATP synthase epsilon subunit. Showing 1 copy in chain L [auth Q].

PF00213
Domain description: ATP synthase delta (OSCP) subunit
Occurring in:
  1. Mitochondrial ATP synthase subunit OSCP
The deposited structure of PDB entry 6rdv contains 1 copy of Pfam domain PF00213 (ATP synthase delta (OSCP) subunit) in Mitochondrial ATP synthase subunit OSCP. Showing 1 copy in chain K [auth P].

InterPro InterPro annotations
IPR000454
Domain description: ATP synthase, F0 complex, subunit C
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
IPR027417
Domain description: P-loop containing nucleoside triphosphate hydrolase
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
IPR020537
Domain description: ATP synthase, F0 complex, subunit C, DCCD-binding site
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
IPR002379
Domain description: V-ATPase proteolipid subunit C-like domain
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
IPR038662
Domain description: F1F0 ATP synthase subunit C superfamily
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
IPR035921
Domain description: F/V-ATP synthase subunit C superfamily
Occurring in:
  1. V-ATPase proteolipid subunit C-like domain-containing protein
IPR005294
Domain description: ATP synthase, F1 complex, alpha subunit
Occurring in:
  1. ATP synthase subunit alpha
IPR000131
Domain description: ATP synthase, F1 complex, gamma subunit
Occurring in:
  1. ATP synthase subunit gamma, mitochondrial
IPR000711
Domain description: ATPase, OSCP/delta subunit
Occurring in:
  1. Mitochondrial ATP synthase subunit OSCP
IPR005722
Domain description: ATP synthase, F1 complex, beta subunit
Occurring in:
  1. ATP synthase subunit beta
IPR000793
Domain description: ATP synthase, alpha subunit, C-terminal
Occurring in:
  1. ATP synthase subunit alpha
IPR020003
Domain description: ATPase, alpha/beta subunit, nucleotide-binding domain, active site
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
IPR000194
Domain description: ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
IPR004100
Domain description: ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
IPR036121
Domain description: ATPase, F1/V1/A1 complex, alpha/beta subunit, N-terminal domain superfamily
Occurring in:
  1. ATP synthase subunit alpha
  2. ATP synthase subunit beta
IPR024034
Domain description: ATPase, F1/V1 complex, beta/alpha subunit, C-terminal
Occurring in:
  1. ATP synthase subunit beta
IPR003593
Domain description: AAA+ ATPase domain
Occurring in:
  1. ATP synthase subunit beta
IPR038376
Domain description: ATP synthase, alpha subunit, C-terminal domain superfamily
Occurring in:
  1. ATP synthase subunit alpha
IPR033732
Domain description: ATP synthase, F1 complex, alpha subunit nucleotide-binding domain
Occurring in:
  1. ATP synthase subunit alpha
IPR023366
Domain description: ATP synthase subunit alpha, N-terminal domain-like superfamily
Occurring in:
  1. ATP synthase subunit alpha
IPR001469
Domain description: ATP synthase, F1 complex, delta/epsilon subunit
Occurring in:
  1. ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein
IPR006721
Domain description: ATP synthase, F1 complex, epsilon subunit, mitochondrial
Occurring in:
  1. epsilon: Polytomella F-ATP synthase epsilon subunit
IPR036771
Domain description: F0F1 ATP synthase delta/epsilon subunit, N-terminal
Occurring in:
  1. ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein
IPR036742
Domain description: ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial
Occurring in:
  1. epsilon: Polytomella F-ATP synthase epsilon subunit
IPR026015
Domain description: F1F0 ATP synthase OSCP/delta subunit, N-terminal domain superfamily
Occurring in:
  1. Mitochondrial ATP synthase subunit OSCP
IPR023632
Domain description: ATP synthase, F1 complex, gamma subunit conserved site
Occurring in:
  1. ATP synthase subunit gamma, mitochondrial
IPR035968
Domain description: ATP synthase, F1 complex, gamma subunit superfamily
Occurring in:
  1. ATP synthase subunit gamma, mitochondrial
IPR020546
Domain description: ATP synthase, F1 complex, delta/epsilon subunit, N-terminal
Occurring in:
  1. ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein
IPR020781
Domain description: ATPase, OSCP/delta subunit, conserved site
Occurring in:
  1. Mitochondrial ATP synthase subunit OSCP

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