› 3zia

X-ray diffraction
2.5Å resolution

The structure of F1-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF1

Released:
DOI: 10.2210/pdb3zia/pdb
PDB entry 3zia coloured by chain, front view.
PDB entry 3zia coloured by chain, side view.
PDB entry 3zia coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
The structure of F₁-ATPase from Saccharomyces cerevisiae inhibited by its regulatory protein IF₁.
Robinson GC, Bason JV, Montgomery MG, Fearnley IM, Mueller DM, Leslie AG, Walker JE
Open Biol 3 120164 (2013)
PMID: 23407639

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 decamer (preferred)
PDBe Complex ID:
PDB-CPX-133629 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
ATP synthase subunit alpha, mitochondrial Chains: A, B, C, K, L, M
Molecule details ›
Chains: A, B, C, K, L, M
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:
Structure domains:
ATP synthase subunit beta, mitochondrial Chains: D, E, F, N, O, P
Molecule details ›
Chains: D, E, F, N, O, P
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:
Structure domains:
ATP synthase subunit gamma, mitochondrial Chains: G, Q
Molecule details ›
Chains: G, Q
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
Structure domains:
ATP synthase subunit delta, mitochondrial Chains: H, R
Molecule details ›
Chains: H, R
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 subunit epsilon, mitochondrial Chains: I, S
Molecule details ›
Chains: I, S
Length: 61 amino acids
Theoretical weight: 6.62 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21306 (Residues: 2-62; Coverage: 98%)
Gene names: ATP15, P0345, YPL271W
Sequence domains: Mitochondrial ATP synthase epsilon chain
Structure domains: ATP synthase, F1 complex, epsilon subunit superfamily, mitochondrial
F(1)-ATPase inhibitor IF(1), mitochondrial Chains: J, T
Molecule details ›
Chains: J, T
Length: 63 amino acids
Theoretical weight: 7.34 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01097 (Residues: 23-85; Coverage: 74%)
Gene names: D1305, INH1, YDL181W
Sequence domains: Mitochondrial ATPase inhibitor, IATP

Ligands and Environments

4 bound ligands:
Ligand ATP 2 x ATP
Ligand MG 10 x MG
Ligand ADP 10 x ADP
Ligand EDO 6 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P21
Unit cell:
a: 118.224Å b: 187.846Å c: 181.812Å
α: 90° β: 89.96° γ: 90°
R-values:
R R work R free
0.226 0.224 0.262
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

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

4 mentions without citation

ATP synthase and Alzheimer's disease: putting a spin on the mitochondrial hypothesis.
Ebanks et al. (2020)
3 more