› 8das

Electron Microscopy
3.5Å resolution

Saccharomyces cerevisiae Ufd1/Npl4/Cdc48 complex bound to two ubiquitin moieties in presence of SUMO-ubiquitin(K48polyUb)-mEOS and ATP, state 1 (intA)

Released:
DOI: 10.2210/pdb8das/pdb
PDB entry 8das coloured by chain, front view.
PDB entry 8das coloured by chain, side view.
PDB entry 8das coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
Lee HG, Lemmon AA, Lima CD
OpenAccess logo Proc Natl Acad Sci U S A 120 e2213703120 (2023)
PMID: 36574706
Related structures: EMD-27274

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)
Assembly name:
PDBe Complex ID:
PDB-CPX-272719 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Cell division control protein 48 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 838 amino acids
Theoretical weight: 92.39 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P25694 (Residues: 1-835; Coverage: 100%)
Gene names: CDC48, YDL126C
Sequence domains:
Nuclear protein localization protein 4 Chain: G
Molecule details ›
Chain: G
Length: 583 amino acids
Theoretical weight: 66.14 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:
Ubiquitin fusion degradation protein 1 Chain: H
Ubiquitin Chains: J, K

Ligands and Environments

3 bound ligands:
Ligand ATP 5 x ATP
Ligand ADP 7 x ADP
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.5Å
Relevant EMDB volumes: EMD-27274
Expression system: Escherichia coli

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Citations

1 review citation

Targeting of client proteins to the VCP/p97/Cdc48 unfolding machine.
Meyer et al. (2023)
3 other articles