4ADY

Crystal structure of 26S proteasome subunit Rpn2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

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This is version 1.2 of the entry. See complete history


Literature

The Structure of the 26S Proteasome Subunit Rpn2 Reveals its Pc Repeat Domain as a Closed Toroid of Two Concentric Alpha-Helical Rings

He, J.Kulkarni, K.Da Fonseca, P.C.A.Krutauz, D.Glickman, M.H.Barford, D.Morris, E.P.

(2012) Structure 20: 513

  • DOI: https://doi.org/10.1016/j.str.2011.12.015
  • Primary Citation of Related Structures:  
    4ADY

  • PubMed Abstract: 

    The 26S proteasome proteolyses ubiquitylated proteins and is assembled from a 20S proteolytic core and two 19S regulatory particles (19S-RP). The 19S-RP scaffolding subunits Rpn1 and Rpn2 function to engage ubiquitin receptors. Rpn1 and Rpn2 are characterized by eleven tandem copies of a 35-40 amino acid repeat motif termed the proteasome/cyclosome (PC) repeat. Here, we reveal that the eleven PC repeats of Rpn2 form a closed toroidal structure incorporating two concentric rings of α helices encircling two axial α helices. A rod-like N-terminal domain consisting of 17 stacked α helices and a globular C-terminal domain emerge from one face of the toroid. Rpn13, an ubiquitin receptor, binds to the C-terminal 20 residues of Rpn2. Rpn1 adopts a similar conformation to Rpn2 but differs in the orientation of its rod-like N-terminal domain. These findings have implications for understanding how 19S-RPs recognize, unfold, and deliver ubiquitylated substrates to the 20S core.


  • Organizational Affiliation

    Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, United Kingdom.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S PROTEASOME REGULATORY SUBUNIT RPN2
A, B
963Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P32565 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32565 
Go to UniProtKB:  P32565
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32565
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.96α = 90
b = 148.66β = 107.39
c = 114.03γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2012-03-21
    Changes: Other
  • Version 1.2: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other