› 6g2z

X-ray diffraction
1.92Å resolution

Crystal structure of the p97 D2 domain in a helical split-washer conformation

Released:
DOI: 10.2210/pdb6g2z/pdb
PDB entry 6g2z coloured by chain, front view.
PDB entry 6g2z coloured by chain, side view.
PDB entry 6g2z coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding.
Stach L, Morgan RM, Makhlouf L, Douangamath A, von Delft F, Zhang X, Freemont PS
FEBS Lett 594 933-943 (2020)
PMID: 31701538

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157169 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Transitional endoplasmic reticulum ATPase Chain: A
Molecule details ›
Chain: A
Length: 306 amino acids
Theoretical weight: 34.23 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P55072 (Residues: 462-764; Coverage: 38%)
Gene names: HEL-220, HEL-S-70, VCP
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MPD 4 x MPD
Ligand DMS 2 x DMS
Ligand ADP 1 x ADP
Ligand NA 1 x NA
Ligand EJW 1 x EJW
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P61
Unit cell:
a: 92.389Å b: 92.389Å c: 65.988Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.224 0.223 0.247
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Targeting of client proteins to the VCP/p97/Cdc48 unfolding machine.
Meyer et al. (2023)
1 more

3 mentions without citation

AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors.
Zhang et al. (2021)
2 more