2X5N

Crystal Structure of the SpRpn10 VWA domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structure of Rpn10 and its Interactions with Polyubiquitin Chains and the Proteasome Subunit Rpn12.

Riedinger, C.Boehringer, J.Trempe, J.F.Lowe, E.D.Brown, N.R.Gehring, K.Noble, M.E.Gordon, C.Endicott, J.A.

(2010) J Biol Chem 285: 33992

  • DOI: https://doi.org/10.1074/jbc.M110.134510
  • Primary Citation of Related Structures:  
    2X5N

  • PubMed Abstract: 

    Schizosaccharomyces pombe Rpn10 (SpRpn10) is a proteasomal ubiquitin (Ub) receptor located within the 19 S regulatory particle where it binds to subunits of both the base and lid subparticles. We have solved the structure of full-length SpRpn10 by determining the crystal structure of the von Willebrand factor type A domain and characterizing the full-length protein by NMR. We demonstrate that the single Ub-interacting motif (UIM) of SpRpn10 forms a 1:1 complex with Lys(48)-linked diUb, which it binds selectively over monoUb and Lys(63)-linked diUb. We further show that the SpRpn10 UIM binds to SpRpn12, a subunit of the lid subparticle, with an affinity comparable with Lys(48)-linked diUb. This is the first observation of a UIM binding other than a Ub fold and suggests that SpRpn12 could modulate the activity of SpRpn10 as a proteasomal Ub receptor.


  • Organizational Affiliation

    Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S PROTEASOME REGULATORY SUBUNIT RPN10192Schizosaccharomyces pombeMutation(s): 0 
UniProt
Find proteins for O94444 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore O94444 
Go to UniProtKB:  O94444
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94444
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • R-Value Observed: 0.125 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.99α = 90
b = 35.23β = 111.2
c = 60.14γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-25
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance