› 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

17 review citations

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

12 mentions without citation

Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis.
Ray et al. (2023)
11 more