› 3zry

X-ray diffraction
6.5Å resolution

Rotor architecture in the F(1)-c(10)-ring complex of the yeast F-ATP synthase

Released:
DOI: 10.2210/pdb3zry/pdb
PDB entry 3zry coloured by chain, front view.
PDB entry 3zry coloured by chain, side view.
PDB entry 3zry coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Rotor architecture in the yeast and bovine F1-c-ring complexes of F-ATP synthase.
Giraud MF, Paumard P, Sanchez C, Brèthes D, Velours J, Dautant A
J Struct Biol 177 490-7 (2012)
PMID: 22119846

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

Assemblies composition:
hetero nonamer (preferred)
homo decamer
Assembly name:
PDBe Complex ID:
PDB-CPX-123199 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
ATP synthase subunit alpha, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 510 amino acids
Theoretical weight: 55.01 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07251 (Residues: 36-545; Coverage: 94%)
Gene names: ATP1, YBL0827, YBL099W
Sequence domains:
ATP synthase subunit beta, mitochondrial Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 478 amino acids
Theoretical weight: 51.18 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00830 (Residues: 34-511; Coverage: 94%)
Gene names: ATP2, J2041, YJR121W
Sequence domains:
ATP synthase subunit gamma, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 278 amino acids
Theoretical weight: 30.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38077 (Residues: 34-311; Coverage: 89%)
Gene names: ATP3, ATP3a, ATP3b, YBR039W, YBR0408
Sequence domains: ATP synthase
ATP synthase subunit delta, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 14.57 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12165 (Residues: 23-160; Coverage: 86%)
Gene names: ATP16, D2935, YD8119.03, YDL004W
Sequence domains:
ATP synthase catalytic sector F1 epsilon subunit Chain: I
Molecule details ›
Chain: I
Length: 61 amino acids
Theoretical weight: 6.64 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: E9P9X4 (Residues: 2-62; Coverage: 98%)
Sequence domains: Mitochondrial ATP synthase epsilon chain
ATP synthase subunit 9, mitochondrial Chains: J, K, L, M, N, O, P, Q, R, S
Molecule details ›
Chains: J, K, L, M, N, O, P, Q, R, S
Length: 76 amino acids
Theoretical weight: 7.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P61829 (Residues: 1-76; Coverage: 100%)
Gene names: ATP9, OLI1, OLI3, PHO2, Q0130
Sequence domains: ATP synthase subunit C

Ligands and Environments

2 bound ligands:
Ligand ANP 5 x ANP
Ligand MG 5 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 107.69Å b: 174.91Å c: 164.26Å
α: 90° β: 93.92° γ: 90°
R-values:
R R work R free
0.318 0.317 0.339

Quick links

Citations

8 review citations

The Mitochondrial Permeability Transition Pore: Channel Formation by F-ATP Synthase, Integration in Signal Transduction, and Role in Pathophysiology.
Bernardi et al. (2015)
7 more

4 mentions without citation

Structure of a mitochondrial ATP synthase with bound native cardiolipin.
Mühleip et al. (2019)
3 more