› 5tj5

Electron Microscopy
3.9Å resolution

Atomic model for the membrane-embedded motor of a eukaryotic V-ATPase

Released:
DOI: 10.2210/pdb5tj5/pdb
PDB entry 5tj5 coloured by chain, front view.
PDB entry 5tj5 coloured by chain, side view.
PDB entry 5tj5 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.
Mazhab-Jafari MT, Rohou A, Schmidt C, Bueler SA, Benlekbir S, Robinson CV, Rubinstein JL
Nature 539 118-122 (2016)
PMID: 27776355
Related structures: EMD-8409

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
PDBe Complex ID:
PDB-CPX-150137 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
V-type proton ATPase subunit a, vacuolar isoform Chain: A
Molecule details ›
Chain: A
Length: 680 amino acids
Theoretical weight: 70.07 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32563 (Residues: 400-829; Coverage: 51%)
Gene names: VPH1, YOR270C
Sequence domains: V-type ATPase 116kDa subunit family
V-type proton ATPase subunit c'' Chain: B
Molecule details ›
Chain: B
Length: 213 amino acids
Theoretical weight: 22.61 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P23968 (Residues: 1-213; Coverage: 100%)
Gene names: PPA1, VMA16, YHR026W
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit c' Chain: D
Molecule details ›
Chain: D
Length: 147 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32842 (Residues: 17-163; Coverage: 90%)
Gene names: CLS9, P1064, TFP3, VMA11, YPL234C
Sequence domains: ATP synthase subunit C
V-type proton ATPase subunit c Chains: E, F, G, H, I, J, M, N
Molecule details ›
Chains: E, F, G, H, I, J, M, N
Length: 150 amino acids
Theoretical weight: 15.22 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25515 (Residues: 9-158; Coverage: 94%)
Gene names: CLS7, CUP5, GEF2, VMA3, YEL027W
Sequence domains: ATP synthase subunit C
Structure domains: lithium bound rotor ring of v- atpase
V-type proton ATPase subunit e Chain: L
Molecule details ›
Chain: L
Length: 57 amino acids
Theoretical weight: 6.48 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q3E7B6 (Residues: 5-61; Coverage: 78%)
Gene names: CWH36, LDB10, VMA9, YCL005W-A
Sequence domains: ATP synthase subunit H
V-type proton ATPase subunit f Chain: O
Molecule details ›
Chain: O
Length: 54 amino acids
Theoretical weight: 4.61 KDa
Source organism: Saccharomyces cerevisiae S288C
V-type proton ATPase subunit d Chain: P
Molecule details ›
Chain: P
Length: 297 amino acids
Theoretical weight: 32.85 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32366 (Residues: 4-341; Coverage: 86%)
Gene names: L9324.8, VMA6, YLR447C
Sequence domains: ATP synthase (C/AC39) subunit

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-8409

Quick links

Citations

27 review citations

Structure and Mechanisms of F-Type ATP Synthases.
Kühlbrandt W. (2019)
26 more

8 mentions without citation

Atomic model for the membrane-embedded VO motor of a eukaryotic V-ATPase.
Mazhab-Jafari et al. (2016)
7 more