› 6oo2

Electron Microscopy
4.4Å resolution

Vps4 with Cyclic Peptide Bound in the Central Pore

Released:
DOI: 10.2210/pdb6oo2/pdb
PDB entry 6oo2 coloured by chain, front view.
PDB entry 6oo2 coloured by chain, side view.
PDB entry 6oo2 coloured by chain, top view.
Source organisms:
Primary publication:
Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.
Han H, Fulcher JM, Dandey VP, Iwasa JH, Sundquist WI, Kay MS, Shen PS, Hill CP
OpenAccess logo Elife 8 (2019)
PMID: 31184588
Related structures: EMD-20142

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero nonadecamer (preferred)
PDBe Complex ID:
PDB-CPX-156669 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Vacuolar protein sorting-associated protein 4 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 337 amino acids
Theoretical weight: 37.12 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: P52917 (Residues: 101-437; Coverage: 77%)
Gene names: CSC1, DID6, END13, GRD13, P9705.10, VPL4, VPS4, VPT10, YPR173C
Sequence domains:
Designed Cyclic Peptide Chain: G
Molecule details ›
Chain: G
Length: 30 amino acids
Theoretical weight: 2.66 KDa
Source organism: synthetic construct
Expression system: Not provided
Vacuolar protein sorting-associated protein VTA1 Chains: H, I, J, K, L, M, N, O, P, Q, R, S
Molecule details ›
Chains: H, I, J, K, L, M, N, O, P, Q, R, S
Length: 51 amino acids
Theoretical weight: 5.77 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
UniProt:
  • Canonical: Q06263 (Residues: 280-330; Coverage: 16%)
Gene names: VTA1, YLR181C
Sequence domains: Vta1 C-terminal domain

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.4Å
Relevant EMDB volumes: EMD-20142
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

7 review citations

Stairway to translocation: AAA+ motor structures reveal the mechanisms of ATP-dependent substrate translocation.
Gates et al. (2020)
6 more

3 mentions without citation

Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases.
Han et al. (2019)
2 more