5U4P

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.

Worden, E.J.Dong, K.C.Martin, A.

(2017) Mol Cell 67: 799-811.e8

  • DOI: 10.1016/j.molcel.2017.07.023
  • Primary Citation of Related Structures:  
    5W83, 5U4P

  • PubMed Abstract: 
  • Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to prevent premature ubiquitin chain removal and substrate escape ...

    Poly-ubiquitin chains direct protein substrates to the 26S proteasome, where they are removed by the deubiquitinase Rpn11 during ATP-dependent substrate degradation. Rapid deubiquitination is required for efficient degradation but must be restricted to committed substrates that are engaged with the ATPase motor to prevent premature ubiquitin chain removal and substrate escape. Here we reveal the ubiquitin-bound structure of Rpn11 from S. cerevisiae and the mechanisms for mechanochemical coupling of substrate degradation and deubiquitination. Ubiquitin binding induces a conformational switch of Rpn11's Insert-1 loop from an inactive closed state to an active β hairpin. This switch is rate-limiting for deubiquitination and strongly accelerated by mechanical substrate translocation into the AAA+ motor. Deubiquitination by Rpn11 and ubiquitin unfolding by the ATPases are in direct competition. The AAA+ motor-driven acceleration of Rpn11 is therefore important to ensure that poly-ubiquitin chains are removed only from committed substrates and fast enough to prevent their co-degradation.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: a.martin@berkeley.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN8A177Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN8YOR261CO5360
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q08723 
Go to UniProtKB:  Q08723
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
26S proteasome regulatory subunit RPN11B220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPN11MPR1YFR004W
EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P43588 
Go to UniProtKB:  P43588
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S31C76Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
UniProt
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P05759 
Go to UniProtKB:  P05759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.21α = 90
b = 126.21β = 90
c = 139.87γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--
Howard Hughes Medical Institute (HHMI)United States--
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-06
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence