› 6rdk

Electron Microscopy
3.7Å resolution

Cryo-EM structure of Polytomella F-ATP synthase, Rotary substate 1B, composite map

Released:
DOI: 10.2210/pdb6rdk/pdb
PDB entry 6rdk coloured by chain, front view.
PDB entry 6rdk coloured by chain, side view.
PDB entry 6rdk coloured by chain, top view.
Source organism: Polytomella sp. Pringsheim 198.80
Primary publication:
Rotary substates of mitochondrial ATP synthase reveal the basis of flexible F1-Fo coupling.
Murphy BJ, Klusch N, Langer J, Mills DJ, Yildiz Ö, Kühlbrandt W
Science 364 (2019)
PMID: 31221832
Related structures: EMD-4821

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O + 4 H(+)(Side 1) = ADP + phosphate + 4 H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 31-mer (preferred)
PDBe Complex ID:
PDB-CPX-100103 (preferred)
Entry contents:
18 distinct polypeptide molecules
Macromolecules (18 distinct):
ASA-10: Polytomella F-ATP synthase associated subunit 10 Chain: 0
Molecule details ›
Chain: 0
Length: 82 amino acids
Theoretical weight: 8.73 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR95 (Residues: 1-82; Coverage: 100%)
ATP synthase associated protein ASA1 Chain: 1
Molecule details ›
Chain: 1
Length: 618 amino acids
Theoretical weight: 68.68 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: Q85JD5 (Residues: 1-618; Coverage: 100%)
Gene name: asa1
Mitochondrial ATP synthase subunit ASA2 Chain: 2
Molecule details ›
Chain: 2
Length: 441 amino acids
Theoretical weight: 44.84 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P6B9 (Residues: 1-383; Coverage: 100%)
Mitochondrial F1F0 ATP synthase associated 32 kDa protein Chain: 3
Molecule details ›
Chain: 3
Length: 325 amino acids
Theoretical weight: 34.85 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: K0J903 (Residues: 1-325; Coverage: 100%)
Gene name: asa3
Mitochondrial ATP synthase associated protein ASA4 Chain: 4
Molecule details ›
Chain: 4
Length: 294 amino acids
Theoretical weight: 31.28 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7NIZ2 (Residues: 1-294; Coverage: 100%)
Gene name: asa4
Mitochondrial F1F0 ATP synthase associated 14 kDa protein Chain: 5
Molecule details ›
Chain: 5
Length: 123 amino acids
Theoretical weight: 14 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A024FSR7 (Residues: 1-123; Coverage: 100%)
Gene name: asa5
Sequence domains: F1F0 ATP synthase subunit ASA5
Mitochondrial ATP synthase subunit ASA6 Chain: 6
Molecule details ›
Chain: 6
Length: 151 amino acids
Theoretical weight: 15.9 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P897 (Residues: 1-151; Coverage: 100%)
Mitochondrial ATP synthase associated protein ASA7 Chain: 7
Molecule details ›
Chain: 7
Length: 190 amino acids
Theoretical weight: 20.55 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I2 (Residues: 1-190; Coverage: 100%)
Mitochondrial ATP synthase subunit ASA8 Chain: 8
Molecule details ›
Chain: 8
Length: 89 amino acids
Theoretical weight: 9.88 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I7 (Residues: 1-89; Coverage: 100%)
ASA-9: Polytomella F-ATP synthase associated subunit 9 Chain: 9
Molecule details ›
Chain: 9
Length: 97 amino acids
Theoretical weight: 11 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR73 (Residues: 1-97; Coverage: 100%)
V-ATPase proteolipid subunit C-like domain-containing protein Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 127 amino acids
Theoretical weight: 12.66 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P7X5 (Residues: 1-127; Coverage: 100%)
Sequence domains: ATP synthase subunit C
F-ATPase protein 6 Chain: M
Molecule details ›
Chain: M
Length: 327 amino acids
Theoretical weight: 34.8 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: H8PGG3 (Residues: 1-327; Coverage: 100%)
Gene name: atp6
Sequence domains: ATP synthase A chain
Mitochondrial ATP synthase subunit OSCP Chain: P
Molecule details ›
Chain: P
Length: 229 amino acids
Theoretical weight: 25.53 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D8V7I1 (Residues: 1-229; Coverage: 100%)
Sequence domains: ATP synthase delta (OSCP) subunit
epsilon: Polytomella F-ATP synthase epsilon subunit Chain: Q
Molecule details ›
Chain: Q
Length: 74 amino acids
Theoretical weight: 8.21 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0A5H1ZR74 (Residues: 1-74; Coverage: 100%)
Sequence domains: Mitochondrial ATP synthase epsilon chain
ATP synthase F1 complex delta/epsilon subunit N-terminal domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 199 amino acids
Theoretical weight: 20.88 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: D7P7X6 (Residues: 1-199; Coverage: 100%)
Sequence domains: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
ATP synthase subunit gamma, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 317 amino acids
Theoretical weight: 34.64 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: Q4LDE7 (Residues: 1-317; Coverage: 100%)
Gene name: atp3
Sequence domains: ATP synthase
ATP synthase subunit alpha Chains: T, U, V
Molecule details ›
Chains: T, U, V
Length: 562 amino acids
Theoretical weight: 60.77 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0ZW40 (Residues: 1-562; Coverage: 100%)
Gene name: atp1
Sequence domains:
ATP synthase subunit beta Chains: X, Y, Z
Molecule details ›
Chains: X, Y, Z
Length: 574 amino acids
Theoretical weight: 61.94 KDa
Source organism: Polytomella sp. Pringsheim 198.80
UniProt:
  • Canonical: A0ZW41 (Residues: 1-574; Coverage: 100%)
Gene name: atp2
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand ZN 1 x ZN
Ligand ATP 3 x ATP
Ligand MG 5 x MG
Ligand ADP 2 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4821

Quick links

Citations

29 review citations

Structure and Mechanisms of F-Type ATP Synthases.
Kühlbrandt W. (2019)
28 more

1 mention without citation

CryoFold: determining protein structures and data-guided ensembles from cryo-EM density maps.
Shekhar et al. (2021)