› 8f39

Electron Microscopy
3.5Å resolution

Yeast ATP synthase in conformation-2, at pH 6

Released:
DOI: 10.2210/pdb8f39/pdb
PDB entry 8f39 coloured by chain, front view.
PDB entry 8f39 coloured by chain, side view.
PDB entry 8f39 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Conformational ensemble of yeast ATP synthase at low pH reveals unique intermediates and plasticity in F1-Fo coupling.
Sharma S, Luo M, Patel H, Mueller DM, Liao M
Nat Struct Mol Biol (2024)
PMID: 38316880
Related structures: EMD-28835

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:

Structure analysis Details

Assembly composition:
hetero 27-mer (preferred)
PDBe Complex ID:
PDB-CPX-133628 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
ATP synthase subunit gamma, mitochondrial Chain: G
Molecule details ›
Chain: G
Length: 261 amino acids
Theoretical weight: 29.04 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38077 (Residues: 38-307; Coverage: 84%)
Gene names: ATP3, ATP3a, ATP3b, YBR039W, YBR0408
Sequence domains: ATP synthase
ATP synthase subunit 4, mitochondrial Chain: Z
Molecule details ›
Chain: Z
Length: 155 amino acids
Theoretical weight: 17.58 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05626 (Residues: 88-242; Coverage: 64%)
Gene names: ATP4, LPF7C, YPL078C
Sequence domains: Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
ATP synthase subunit d, mitochondrial Chain: 7
Molecule details ›
Chain: 7
Length: 171 amino acids
Theoretical weight: 19.51 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P30902 (Residues: 4-174; Coverage: 98%)
Gene names: ATP7, YKL016C
Sequence domains: ATP synthase D chain, mitochondrial (ATP5H)
ATP synthase subunit H, mitochondrial Chain: 6
Molecule details ›
Chain: 6
Length: 89 amino acids
Theoretical weight: 10.09 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12349 (Residues: 36-124; Coverage: 72%)
Gene names: ATP14, L8003.20, YLR295C
Sequence domains: ATP synthase complex subunit h
ATP synthase subunit f, mitochondrial Chain: U
Molecule details ›
Chain: U
Length: 85 amino acids
Theoretical weight: 9.38 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q06405 (Residues: 7-91; Coverage: 84%)
Gene names: ATP17, D9481.21, YDR377W
Sequence domains: Mitochondrial F1-F0 ATP synthase subunit F of fungi
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: 75 amino acids
Theoretical weight: 7.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P61829 (Residues: 1-75; Coverage: 99%)
Gene names: ATP9, OLI1, OLI3, PHO2, Q0130
Sequence domains: ATP synthase subunit C
ATP synthase protein 8 Chain: 8
Molecule details ›
Chain: 8
Length: 41 amino acids
Theoretical weight: 5.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00856 (Residues: 7-47; Coverage: 85%)
Gene names: AAP1, ATP8, Q0080
Sequence domains: Fungal ATP synthase protein 8 (A6L)
ATP synthase subunit a Chain: X
Molecule details ›
Chain: X
Length: 224 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00854 (Residues: 36-259; Coverage: 87%)
Gene names: ATP6, OLI2, OLI4, PHO1, Q0085
Sequence domains: ATP synthase A chain
ATP synthase subunit J, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 37 amino acids
Theoretical weight: 4.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P81450 (Residues: 1-37; Coverage: 63%)
Gene names: ATP18, YML081BC, YML081C-A
Sequence domains: ATP synthase j chain
ATP synthase subunit 5, mitochondrial Chain: Y
Molecule details ›
Chain: Y
Length: 166 amino acids
Theoretical weight: 17.83 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P09457 (Residues: 24-189; Coverage: 78%)
Gene names: ATP5, D9740.11, OSCP, YDR298C
Sequence domains: ATP synthase delta (OSCP) subunit
ATP synthase subunit alpha, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 507 amino acids
Theoretical weight: 54.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P07251 (Residues: 39-545; Coverage: 93%)
Gene names: ATP1, YBL0827, YBL099W
Sequence domains:
ATP synthase subunit beta, mitochondrial Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 473 amino acids
Theoretical weight: 50.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P00830 (Residues: 39-511; Coverage: 93%)
Gene names: ATP2, J2041, YJR121W
Sequence domains:
ATP synthase subunit delta, mitochondrial Chain: H
Molecule details ›
Chain: H
Length: 132 amino acids
Theoretical weight: 14.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12165 (Residues: 29-160; Coverage: 83%)
Gene names: ATP16, D2935, YD8119.03, YDL004W
Sequence domains:
ATP synthase subunit epsilon, mitochondrial Chain: I
Molecule details ›
Chain: I
Length: 59 amino acids
Theoretical weight: 6.39 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21306 (Residues: 2-60; Coverage: 95%)
Gene names: ATP15, P0345, YPL271W
Sequence domains: Mitochondrial ATP synthase epsilon chain

Ligands and Environments

2 bound ligands:
Ligand ADP 5 x ADP
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-28835

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