› 8i6v

Electron Microscopy
3.06Å resolution

Cryo-EM structure of the polyphosphate polymerase VTC complex(Vtc4/Vtc3/Vtc1)

Released:
DOI: 10.2210/pdb8i6v/pdb
PDB entry 8i6v coloured by chain, front view.
PDB entry 8i6v coloured by chain, side view.
PDB entry 8i6v coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Cryo-EM structure of the polyphosphate polymerase VTC reveals coupling of polymer synthesis to membrane transit.
Liu W, Wang J, Comte-Miserez V, Zhang M, Yu X, Chen Q, Jessen HJ, Mayer A, Wu S, Ye S
EMBO J 42 e113320 (2023)
PMID: 37066886
Related structures: EMD-35208

Function and Biology Details

Reaction catalysed: 
ATP + (phosphate)(n) = ADP + (phosphate)(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154011 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Vacuolar transporter chaperone complex subunit 1 Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 129 amino acids
Theoretical weight: 14.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40046 (Residues: 1-129; Coverage: 100%)
Gene names: NRF1, PHM4, VTC1, YER072W
Sequence domains: Domain of unknown function (DUF202)
Vacuolar transporter chaperone 3 complex subunit 3 Chain: D
Molecule details ›
Chain: D
Length: 835 amino acids
Theoretical weight: 96.68 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02725 (Residues: 1-835; Coverage: 100%)
Gene names: PHM2, VTC3, YPL019C
Sequence domains:
Vacuolar transporter chaperone complex subunit 4 Chain: E
Molecule details ›
Chain: E
Length: 721 amino acids
Theoretical weight: 83.27 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P47075 (Residues: 1-721; Coverage: 100%)
Gene names: J1345, PHM3, VTC4, YJL012C
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand POV 1 x POV
Ligand PO4 3 x PO4
Ligand 3PO 1 x 3PO
Ligand MN 1 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.06Å
Relevant EMDB volumes: EMD-35208
Expression system: Saccharomyces cerevisiae

Quick links

Citations

2 review citations

Advances in the cellular biology, biochemistry, and molecular biology of acidocalcisomes.
Docampo R. (2024)
1 more