› 4ocn

X-ray diffraction
2.25Å resolution

Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II

Released:
DOI: 10.2210/pdb4ocn/pdb
PDB entry 4ocn coloured by chain, front view.
PDB entry 4ocn coloured by chain, side view.
PDB entry 4ocn coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11.
Pathare GR, Nagy I, Śledź P, Anderson DJ, Zhou HJ, Pardon E, Steyaert J, Förster F, Bracher A, Baumeister W
Proc Natl Acad Sci U S A 111 2984-9 (2014)
PMID: 24516147

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

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211249 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
26S proteasome regulatory subunit RPN8 Chains: A, D
Molecule details ›
Chains: A, D
Length: 187 amino acids
Theoretical weight: 20.84 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08723 (Residues: 1-185; Coverage: 55%)
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 Chains: B, E
Molecule details ›
Chains: B, E
Length: 220 amino acids
Theoretical weight: 24.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P43588 (Residues: 1-220; Coverage: 72%)
Gene names: MPR1, RPN11, YFR004W
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Structure domains: Cytidine Deaminase, domain 2
Nb1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 133 amino acids
Theoretical weight: 14.85 KDa
Source organism: Lama glama
Expression system: Escherichia coli
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P43212
Unit cell:
a: 80.042Å b: 80.042Å c: 386.205Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.235 0.232 0.281
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli

Quick links

Citations

38 review citations

Mechanisms of Deubiquitinase Specificity and Regulation.
Mevissen et al. (2017)
37 more

2 mentions without citation

Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11.
Pathare et al. (2014)
1 more