4O8X | pdb_00004o8x

Zinc-bound Rpn11 in complex with Rpn8

• PDB DOI: https://doi.org/10.2210/pdb4O8X/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-12-30 Released: 2014-01-22 
• Deposition Author(s): Worden, E.J., Padovani, C., Martin, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free: 
  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

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

• PubMed: 24463465 
• DOI: https://doi.org/10.1038/nsmb.2771
• Primary Citation Related Structures: 
  4O8X, 4O8Y


• 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 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.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.
1] Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA. [2] California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.92 kDa 
• Atom Count: 3,082 
• Modeled Residue Count: 340 
• Deposited Residue Count: 425 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN8	A	185	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN8, YOR261C, O5360
UniProt
Find proteins for Q08723 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08723  Go to UniProtKB:  Q08723

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN11	B	240	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: RPN11, MPR1, YFR004W EC: 3.4.19.12
UniProt
Find proteins for P43588 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43588  Go to UniProtKB:  P43588

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	HA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	AA [auth B], BA [auth B], C [auth A], CA [auth B], D [auth A], DA [auth B], E [auth A], EA [auth B], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.99 Å
• R-Value Free:  0.195 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.296	α = 90
b = 70.296	β = 90
c = 198.912	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Worden, E.J., Padovani, C., Martin, A.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2014-02-26
  Changes: Database references
• Version 1.2: 2014-03-19
  Changes: Database references
• Version 1.3: 2017-11-22
  Changes: Refinement description
• Version 1.4: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description