› 6j5j

Electron Microscopy
3.45Å resolution

Cryo-EM structure of the mammalian E-state ATP synthase

Released:
DOI: 10.2210/pdb6j5j/pdb
PDB entry 6j5j coloured by chain, front view.
PDB entry 6j5j coloured by chain, side view.
PDB entry 6j5j coloured by chain, top view.
Source organism: Sus scrofa
Primary publication:
Cryo-EM structure of the mammalian ATP synthase tetramer bound with inhibitory protein IF1.
Gu J, Zhang L, Zong S, Guo R, Liu T, Yi J, Wang P, Zhuo W, Yang M
Science 364 1068-1075 (2019)
PMID: 31197009
Related structures: EMD-0669

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-236719 (preferred)
Entry contents:
19 distinct polypeptide molecules
Macromolecules (19 distinct):
ATP synthase subunit alpha, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 509 amino acids
Theoretical weight: 55.17 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P80021 (Residues: 45-553; Coverage: 92%)
Gene names: ATP5A1, ATP5A2, ATP5F1A
Sequence domains:
ATP synthase subunit beta Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 469 amino acids
Theoretical weight: 50.61 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: K7GLT8 (Residues: 101-569; Coverage: 82%)
Gene name: ATP5F1B
Sequence domains:
ATPase inhibitor, mitochondrial Chain: J
Molecule details ›
Chain: J
Length: 83 amino acids
Theoretical weight: 9.5 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q29307 (Residues: 26-108; Coverage: 77%)
Gene names: ATP5IF1, ATPI, ATPIF1
Sequence domains: Mitochondrial ATPase inhibitor, IATP
ATP synthase subunit gamma Chain: G
Molecule details ›
Chain: G
Length: 272 amino acids
Theoretical weight: 30.12 KDa
Source organism: Sus scrofa
ATP synthase F1 subunit delta Chain: H
Molecule details ›
Chain: H
Length: 132 amino acids
Theoretical weight: 13.85 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A286ZYL7 (Residues: 36-167; Coverage: 79%)
Gene name: ATP5F1D
Sequence domains:
ATP synthase, H+ transporting, mitochondrial F1 complex, epsilon subunit Chain: I
Molecule details ›
Chain: I
Length: 48 amino acids
Theoretical weight: 5.37 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A5GFX4 (Residues: 2-49; Coverage: 94%)
Gene names: ATP5E, CH242-247L10.5-002
Sequence domains: Mitochondrial ATP synthase epsilon chain
ATP synthase subunit O, mitochondrial Chain: S
Molecule details ›
Chain: S
Length: 187 amino acids
Theoretical weight: 20.56 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q2EN81 (Residues: 24-210; Coverage: 88%)
Gene names: ATP5O, ATP5PO
Sequence domains: ATP synthase delta (OSCP) subunit
ATP synthase subunit b Chain: b
Molecule details ›
Chain: b
Length: 209 amino acids
Theoretical weight: 24 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D0MI69 (Residues: 45-253; Coverage: 82%)
Gene name: ATP5PB
Sequence domains: Mitochondrial ATP synthase B chain precursor (ATP-synt_B)
ATP synthase-coupling factor 6, mitochondrial Chain: c
Molecule details ›
Chain: c
Length: 70 amino acids
Theoretical weight: 8.25 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P13618 (Residues: 7-76; Coverage: 92%)
Gene names: ATP5J, ATP5PF
Sequence domains: Mitochondrial ATP synthase coupling factor 6
ATP synthase subunit d, mitochondrial Chain: d
Molecule details ›
Chain: d
Length: 147 amino acids
Theoretical weight: 16.9 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287B4I0 (Residues: 4-73, 74-126; Coverage: 90%)
Gene name: ATP5PD
Sequence domains: ATP synthase D chain, mitochondrial (ATP5H)
ATP synthase subunit e Chain: e
Molecule details ›
Chain: e
Length: 63 amino acids
Theoretical weight: 5.38 KDa
Source organism: Sus scrofa
ATP synthase subunit f, mitochondrial Chain: f
Molecule details ›
Chain: f
Length: 87 amino acids
Theoretical weight: 10.2 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q95339 (Residues: 2-88; Coverage: 99%)
Gene names: ATP5J2, ATP5MF
Sequence domains: Mitochondrial F1F0-ATP synthase, subunit f
ATP synthase subunit g Chain: g
Molecule details ›
Chain: g
Length: 84 amino acids
Theoretical weight: 7.17 KDa
Source organism: Sus scrofa
ATP synthase membrane subunit K, mitochondrial Chain: i
Molecule details ›
Chain: i
Length: 42 amino acids
Theoretical weight: 4.86 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TQQ5 (Residues: 9-50; Coverage: 72%)
Gene names: ATP5MD, ATP5MK
Sequence domains: ATP synthase regulation
subunit k analog Chain: k
Molecule details ›
Chain: k
Length: 29 amino acids
Theoretical weight: 2.49 KDa
Source organism: Sus scrofa
ATP synthase protein 8 Chain: 8
Molecule details ›
Chain: 8
Length: 67 amino acids
Theoretical weight: 7.95 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q35914 (Residues: 1-67; Coverage: 100%)
Gene names: ATP8, ATPASE8, MT-ATP8, MTATP8
Sequence domains: ATP synthase protein 8
ATP synthase subunit a Chain: a
Molecule details ›
Chain: a
Length: 226 amino acids
Theoretical weight: 25.05 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q35915 (Residues: 1-226; Coverage: 100%)
Gene names: ATP6, ATPASE6, MT-ATP6, MTATP6
Sequence domains: ATP synthase A chain
ATP synthase lipid-binding protein Chains: K, L, M, N, O, P, Q, R
Molecule details ›
Chains: K, L, M, N, O, P, Q, R
Length: 72 amino acids
Theoretical weight: 7.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: Q4VT52 (Residues: 63-134; Coverage: 53%)
Sequence domains: ATP synthase subunit C
ATP synthase membrane subunit 6.8PL Chain: u
Molecule details ›
Chain: u
Length: 42 amino acids
Theoretical weight: 3.59 KDa
Source organism: Sus scrofa

Ligands and Environments

3 bound ligands:
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: 3.45Å
Relevant EMDB volumes: EMD-0669

Quick links

Citations

30 review citations

The assembly, regulation and function of the mitochondrial respiratory chain.
Vercellino et al. (2022)
29 more

3 mentions without citation

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