› 6oa9

Electron Microscopy
3.9Å resolution

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

Released:
DOI: 10.2210/pdb6oa9/pdb
PDB entry 6oa9 coloured by chain, front view.
PDB entry 6oa9 coloured by chain, side view.
PDB entry 6oa9 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.
Twomey EC, Ji Z, Wales TE, Bodnar NO, Ficarro SB, Marto JA, Engen JR, Rapoport TA
Science 365 (2019)
PMID: 31249135
Related structures: EMD-0665

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-143481 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Cell division control protein 48 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 835 amino acids
Theoretical weight: 92.11 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P25694 (Residues: 1-835; Coverage: 100%)
Gene names: CDC48, YDL126C
Sequence domains:
Ubiquitin Chains: H, J, K
Molecule details ›
Chains: H, J, K
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CH08 (Residues: 1-76; Coverage: 59%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains: Ubiquitin family
Nuclear protein localization protein 4 Chain: G
Molecule details ›
Chain: G
Length: 580 amino acids
Theoretical weight: 65.86 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P33755 (Residues: 1-580; Coverage: 100%)
Gene names: HRD4, NPL4, YBR1231, YBR170C
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand ATP 9 x ATP
Ligand ADP 1 x ADP
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.9Å
Relevant EMDB volumes: EMD-0665
Expression system: Escherichia coli

Quick links

Citations

38 review citations

Protein quality control in the secretory pathway.
Sun et al. (2019)
37 more

8 mentions without citation

AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms.
Zhang et al. (2020)
7 more