› 4dl0

X-ray diffraction
2.9Å resolution

Crystal Structure of the heterotrimeric EGChead Peripheral Stalk Complex of the Yeast Vacuolar ATPase

Released:
DOI: 10.2210/pdb4dl0/pdb
PDB entry 4dl0 coloured by chain, front view.
PDB entry 4dl0 coloured by chain, side view.
PDB entry 4dl0 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Crystal structure of the yeast vacuolar ATPase heterotrimeric EGC(head) peripheral stalk complex.
Oot RA, Huang LS, Berry EA, Wilkens S
Structure 20 1881-92 (2012)
PMID: 23000382

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149534 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
V-type proton ATPase subunit C Chains: C, I
Molecule details ›
Chains: C, I
Length: 130 amino acids
Theoretical weight: 14.59 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P31412 (Residues: 158-277; Coverage: 31%)
Gene names: VAT3, VATC, VMA5, YKL080W, YKL410
Sequence domains: V-ATPase subunit C
Structure domains: Alpha-Beta Plaits
V-type proton ATPase subunit G Chains: G, K
Molecule details ›
Chains: G, K
Length: 119 amino acids
Theoretical weight: 13.22 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P48836 (Residues: 1-114; Coverage: 100%)
Gene names: VMA10, YHR039BC, YHR039C-A, YHR039C-B
Sequence domains: Vacuolar (H+)-ATPase G subunit
Structure domains: Single alpha-helices involved in coiled-coils or other helix-helix interfaces
V-type proton ATPase subunit E Chains: E, J
Molecule details ›
Chains: E, J
Length: 233 amino acids
Theoretical weight: 26.51 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P22203 (Residues: 1-233; Coverage: 100%)
Gene names: O6241, VAT5, VMA4, YOR332W
Sequence domains: ATP synthase (E/31 kDa) subunit
Structure domains: ATP synthase, E subunit, C-terminal

Ligands and Environments

2 bound ligands:
Ligand SO4 8 x SO4
Ligand PBM 2 x PBM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 95.79Å b: 105.611Å c: 120.486Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.212 0.208 0.257
Expression system: Escherichia coli BL21

Quick links

Citations

9 review citations

Eukaryotic V-ATPase: novel structural findings and functional insights.
Marshansky et al. (2014)
8 more

8 mentions without citation

Breaking up and making up: The secret life of the vacuolar H+ -ATPase.
Oot et al. (2017)
7 more