› 5lqz

Electron Microscopy
7Å resolution

Structure of F-ATPase from Pichia angusta, state1

Released:
DOI: 10.2210/pdb5lqz/pdb
PDB entry 5lqz coloured by chain, front view.
PDB entry 5lqz coloured by chain, side view.
PDB entry 5lqz coloured by chain, top view.
Source organism: Ogataea angusta
Primary publication:
Structure of the mitochondrial ATP synthase from Pichia angusta determined by electron cryo-microscopy.
Vinothkumar KR, Montgomery MG, Liu S, Walker JE
Proc Natl Acad Sci U S A 113 12709-12714 (2016)
PMID: 27791192
Related structures: EMD-4102

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 30-mer (preferred)
PDBe Complex ID:
PDB-CPX-123063 (preferred)
Entry contents:
17 distinct polypeptide molecules
Macromolecules (17 distinct):
ATP synthase subunit f Chain: 1
Molecule details ›
Chain: 1
Length: 30 amino acids
Theoretical weight: 2.57 KDa
Source organism: Ogataea angusta
ATP synthase subunit AAP1 Chain: 2
Molecule details ›
Chain: 2
Length: 25 amino acids
Theoretical weight: 2.15 KDa
Source organism: Ogataea angusta
ATP synthase subunit a Chain: 3
Molecule details ›
Chain: 3
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Ogataea angusta
ATP synthase subunit b Chain: 4
Molecule details ›
Chain: 4
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Ogataea angusta
ATP synthase subunit alpha Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 510 amino acids
Theoretical weight: 55.01 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1Q6W1 (Residues: 38-547; Coverage: 93%)
Gene name: HPODL_02577
Sequence domains:
ATP synthase subunit beta Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 476 amino acids
Theoretical weight: 50.85 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1QA59 (Residues: 28-503; Coverage: 95%)
Gene name: HPODL_01806
Sequence domains:
ATP synthase subunit gamma Chain: G
Molecule details ›
Chain: G
Length: 269 amino acids
Theoretical weight: 29.42 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1QGS3 (Residues: 19-287; Coverage: 94%)
Gene name: HPODL_00669
Sequence domains: ATP synthase
ATP synthase subunit delta, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 138 amino acids
Theoretical weight: 14.17 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1QBD1 (Residues: 24-161; Coverage: 86%)
Gene name: HPODL_01793
Sequence domains:
ATP synthase epsilon subunit Chain: I
Molecule details ›
Chain: I
Length: 63 amino acids
Theoretical weight: 6.91 KDa
Source organism: Ogataea angusta
ATPase inhibitor, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 66 amino acids
Theoretical weight: 7.46 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: P01096 (Residues: 26-85; Coverage: 55%)
Gene names: ATP5IF1, ATPI, ATPIF1
Sequence domains: Mitochondrial ATPase inhibitor, IATP
ATP synthase subunit 9, mitochondrial Chains: K, L, M, N, O, P, Q, R, S, T
Molecule details ›
Chains: K, L, M, N, O, P, Q, R, S, T
Length: 76 amino acids
Theoretical weight: 7.84 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: E7E832 (Residues: 1-76; Coverage: 100%)
Gene names: HPOM_08, atp9
Sequence domains: ATP synthase subunit C
ATP synthase subunit 5, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 194 amino acids
Theoretical weight: 20.68 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1QCI5 (Residues: 12-205; Coverage: 95%)
Gene name: HPODL_04372
Sequence domains: ATP synthase delta (OSCP) subunit
ATP synthase subunit 4 Chain: V
Molecule details ›
Chain: V
Length: 204 amino acids
Theoretical weight: 22.29 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1Q9V2 (Residues: 28-231; Coverage: 88%)
Gene name: HPODL_02801
Sequence domains: Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
ATP synthase subunit d, mitochondrial Chain: W
Molecule details ›
Chain: W
Length: 155 amino acids
Theoretical weight: 16.43 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: W1Q731 (Residues: 2-128; Coverage: 73%)
Gene name: HPODL_02723
Sequence domains: ATP synthase D chain, mitochondrial (ATP5H)
ATP synthase subunit h Chain: X
Molecule details ›
Chain: X
Length: 21 amino acids
Theoretical weight: 1.81 KDa
Source organism: Ogataea angusta
ATP synthase subunit a Chain: Y
Molecule details ›
Chain: Y
Length: 252 amino acids
Theoretical weight: 27.56 KDa
Source organism: Ogataea angusta
UniProt:
  • Canonical: E7E837 (Residues: 8-259; Coverage: 97%)
Gene names: HPOM_13, atp6
Sequence domains: ATP synthase A chain
ATP synthase subunit a Chain: Z
Molecule details ›
Chain: Z
Length: 44 amino acids
Theoretical weight: 3.76 KDa
Source organism: Ogataea angusta

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 7Å
Relevant EMDB volumes: EMD-4102

Quick links

Citations

10 review citations

The mitochondrial permeability transition: Recent progress and open questions.
Bernardi et al. (2022)
9 more

4 mentions without citation

In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology.
Chavez et al. (2022)
3 more