› 5u4p

X-ray diffraction
2.5Å resolution

Protein-protein complex between 26S proteasome regulatory subunit RPN8, RPN11, and Ubiquitin S31

Released:
DOI: 10.2210/pdb5u4p/pdb
PDB entry 5u4p coloured by chain, front view.
PDB entry 5u4p coloured by chain, side view.
PDB entry 5u4p coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.
Worden EJ, Dong KC, Martin A
Mol Cell 67 799-811.e8 (2017)
PMID: 28844860

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
PDBe Complex ID:
PDB-CPX-138762 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
26S proteasome regulatory subunit RPN8 Chain: A
Molecule details ›
Chain: A
Length: 177 amino acids
Theoretical weight: 20.15 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q08723 (Residues: 1-177; Coverage: 52%)
Gene names: O5360, RPN8, YOR261C
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Structure domains: Cytidine Deaminase, domain 2
Ubiquitin carboxyl-terminal hydrolase RPN11 Chain: B
Molecule details ›
Chain: B
Length: 220 amino acids
Theoretical weight: 24.46 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P43588 (Residues: 2-219; Coverage: 71%)
Gene names: MPR1, RPN11, YFR004W
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P05759 (Residues: 1-76; Coverage: 50%)
Gene names: L9470.14, RPS31, RPS37, UBI3, YLR167W
Sequence domains: Ubiquitin family

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.3.1
Spacegroup: P6522
Unit cell:
a: 126.21Å b: 126.21Å c: 139.87Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.212 0.211 0.234
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
18 more

10 mentions without citation

Structure and Function of the 26S Proteasome.
Bard et al. (2018)
9 more