2X5N

Crystal Structure of the SpRpn10 VWA domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 

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: 10.1074/jbc.M110.134510

  • 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 de ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
26S PROTEASOME REGULATORY SUBUNIT RPN10
A
192Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: rpn10 (pus1)
Find proteins for O94444 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  O94444
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.123 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 79.990α = 90.00
b = 35.230β = 111.20
c = 60.140γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
SHELXEphasing
SHELXDphasing
PHENIXrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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