4O8X

Zinc-bound Rpn11 in complex with Rpn8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.991 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation.

Worden, E.J.Padovani, C.Martin, A.

(2014) Nat.Struct.Mol.Biol. 21: 220-227

  • DOI: 10.1038/nsmb.2771
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Polyubiquitin chains target protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 to allow efficient substrate degradation. Despite Rpn11's essential function during substrate processing, its detailed structural ...

    Polyubiquitin chains target protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 to allow efficient substrate degradation. Despite Rpn11's essential function during substrate processing, its detailed structural and biochemical characterization has been hindered by difficulties in purifying the isolated enzyme. Here we report the 2.0-Å crystal structures of Zn(2+)-free and Zn(2+)-bound Saccharomyces cerevisiae Rpn11 in an MPN-domain heterodimer with Rpn8. The Rpn11-Rpn8 interaction occurs via two distinct interfaces that may be conserved in related MPN-domain complexes. Our structural and mutational studies reveal that Rpn11 lacks a conserved surface to bind the ubiquitin Ile44 patch, does not interact with the moiety on the proximal side of the scissile isopeptide bond and exhibits no linkage specificity for ubiquitin cleavage. These findings explain how Rpn11 functions as a promiscuous deubiquitinase for cotranslocational substrate deubiquitination during proteasomal degradation.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN8
A
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN8
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08723
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
26S proteasome regulatory subunit RPN11
B
240Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPN11 (MPR1)
EC: 3.4.19.12
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P43588
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.991 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.161 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.296α = 90.00
b = 70.296β = 90.00
c = 198.912γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
SCALEPACKdata scaling
PHENIXrefinement
PHASERphasing
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-22
    Type: Initial release
  • Version 1.1: 2014-02-26
    Type: Database references
  • Version 1.2: 2014-03-19
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description