3VL1 | pdb_00003vl1

Crystal structure of yeast Rpn14

• PDB DOI: https://doi.org/10.2210/pdb3VL1/pdb

• Classification: CHAPERONE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-28 Released: 2012-05-02 
• Deposition Author(s): Kim, S., Nishide, A., Saeki, Y., Takagi, K., Tanaka, K., Kato, K., Mizushima, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.152 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

New crystal structure of the proteasome-dedicated chaperone Rpn14 at 1.6 A resolution

Kim, S., Nishide, A., Saeki, Y., Takagi, K., Tanaka, K., Kato, K., Mizushima, T.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 517-521

• PubMed: 22691779 
• DOI: https://doi.org/10.1107/S1744309112011359
• Primary Citation Related Structures: 
  3VL1


• PubMed Abstract: 
  

  The 26S proteasome is an ATP-dependent protease responsible for selective degradation of polyubiquitylated proteins. Recent studies have suggested that proteasome assembly is a highly ordered multi-step process assisted by specific chaperones. Rpn14, an assembly chaperone for ATPase-ring formation, specifically recognizes the ATPase subunit Rpt6. The structure of Rpn14 at 2.0 Å resolution in space group P6(4) has previously been reported, but the detailed mechanism of Rpn14 function remains unclear. Here, a new crystal structure of Rpn14 with an E384A mutation is presented in space group P2(1) at 1.6 Å resolution. This high-resolution structure provides a framework for understanding proteasome assembly.

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Organizational Affiliation: 
• Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.32 kDa 
• Atom Count: 7,164 
• Modeled Residue Count: 832 
• Deposited Residue Count: 840 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit RPN14	A, B	420	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: RPN14
UniProt
Find proteins for P53196 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53196  Go to UniProtKB:  P53196

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.235 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.152 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.491	α = 90
b = 141.443	β = 95.67
c = 50.491	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-02 
Deposition Author(s): Kim, S., Nishide, A., Saeki, Y., Takagi, K., Tanaka, K., Kato, K., Mizushima, T.

Revision History  

• Version 1.0: 2012-05-02
  Type: Initial release
  
• Version 1.1: 2013-08-14
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Refinement description