› 5dn6

X-ray diffraction
3.98Å resolution

ATP synthase from Paracoccus denitrificans

Released:
DOI: 10.2210/pdb5dn6/pdb
PDB entry 5dn6 coloured by chain, front view.
PDB entry 5dn6 coloured by chain, side view.
PDB entry 5dn6 coloured by chain, top view.
Source organism: Paracoccus denitrificans
Primary publication:
Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 Å resolution.
Morales-Rios E, Montgomery MG, Leslie AG, Walker JE
Proc Natl Acad Sci U S A 112 13231-6 (2015)
PMID: 26460036

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 29-mer (preferred)
PDBe Complex ID:
PDB-CPX-106565 (preferred)
Entry contents:
14 distinct polypeptide molecules
Macromolecules (14 distinct):
Chain A Chain: 1
Molecule details ›
Chain: 1
Length: 20 amino acids
Theoretical weight: 1.72 KDa
Source organism: Paracoccus denitrificans
Chain B Chain: 2
Molecule details ›
Chain: 2
Length: 15 amino acids
Theoretical weight: 1.29 KDa
Source organism: Paracoccus denitrificans
Chain C Chain: 3
Molecule details ›
Chain: 3
Length: 19 amino acids
Theoretical weight: 1.64 KDa
Source organism: Paracoccus denitrificans
ATP synthase subunit alpha Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 511 amino acids
Theoretical weight: 55.1 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B8N8 (Residues: 1-511; Coverage: 100%)
Gene names: Pden_3816, atpA
Sequence domains:
Structure domains:
ATP synthase subunit beta Chains: D, E, F
Molecule details ›
Chains: D, E, F
Length: 474 amino acids
Theoretical weight: 50.39 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B8P0 (Residues: 1-474; Coverage: 100%)
Gene names: Pden_3818, atpD
Sequence domains:
Structure domains:
ATP synthase gamma chain Chain: G
Molecule details ›
Chain: G
Length: 290 amino acids
Theoretical weight: 31.64 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B8N9 (Residues: 1-290; Coverage: 100%)
Gene names: Pden_3817, atpG
Sequence domains: ATP synthase
Structure domains:
ATP synthase subunit delta Chain: H
Molecule details ›
Chain: H
Length: 188 amino acids
Theoretical weight: 20.05 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B8N7 (Residues: 1-188; Coverage: 100%)
Gene names: Pden_3815, atpH
Sequence domains: ATP synthase delta (OSCP) subunit
ATP synthase epsilon chain Chain: I
Molecule details ›
Chain: I
Length: 148 amino acids
Theoretical weight: 15.84 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B8P1 (Residues: 1-148; Coverage: 100%)
Gene names: Pden_3819, atpC
Sequence domains: ATP synthase, Delta/Epsilon chain, beta-sandwich domain
Structure domains: F0F1 ATP synthase delta/epsilon subunit, N-terminal
ATP synthase subunit c Chains: J, K, L, M, N, O, P, Q, R, S, T, U
Molecule details ›
Chains: J, K, L, M, N, O, P, Q, R, S, T, U
Length: 77 amino acids
Theoretical weight: 7.61 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B618 (Residues: 1-77; Coverage: 100%)
Gene names: Pden_2878, atpE
Sequence domains: ATP synthase subunit C
Structure domains: F1F0 ATP synthase subunit C
Chain V Chain: V
Molecule details ›
Chain: V
Length: 78 amino acids
Theoretical weight: 6.66 KDa
Source organism: Paracoccus denitrificans
Chain W Chain: W
Molecule details ›
Chain: W
Length: 124 amino acids
Theoretical weight: 10.57 KDa
Source organism: Paracoccus denitrificans
ATP synthase subunit a Chain: X
Molecule details ›
Chain: X
Length: 283 amino acids
Theoretical weight: 29.72 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B619 (Residues: 1-248; Coverage: 100%)
Gene names: Pden_2879, atpB
Sequence domains: ATP synthase A chain
Chain Y Chain: Y
Molecule details ›
Chain: Y
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Paracoccus denitrificans
DUF1476 domain-containing protein Chain: Z
Molecule details ›
Chain: Z
Length: 104 amino acids
Theoretical weight: 11.69 KDa
Source organism: Paracoccus denitrificans
UniProt:
  • Canonical: A1B602 (Residues: 1-104; Coverage: 100%)
Gene name: Pden_2862
Sequence domains: ATPase inhibitor subunit zeta

Ligands and Environments

3 bound ligands:
Ligand ATP 4 x ATP
Ligand MG 5 x MG
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P21
Unit cell:
a: 112.001Å b: 187.943Å c: 164.724Å
α: 90° β: 97.44° γ: 90°
R-values:
R R work R free
0.297 0.295 0.324

Quick links

Citations

18 review citations

Shared Molecular Mechanisms of Membrane Transporters.
Drew et al. (2016)
17 more

12 mentions without citation

Evolution of the Inhibitory and Non-Inhibitory ε, ζ, and IF1 Subunits of the F1FO-ATPase as Related to the Endosymbiotic Origin of Mitochondria.
Mendoza-Hoffmann et al. (2022)
11 more