2R2Y

Crystal structure of the proteasomal Rpn13 PRU-domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ubiquitin docking at the proteasome through a novel pleckstrin-homology domain interaction.

Schreiner, P.Chen, X.Husnjak, K.Randles, L.Zhang, N.Elsasser, S.Finley, D.Dikic, I.Walters, K.J.Groll, M.

(2008) Nature 453: 548-552

  • DOI: 10.1038/nature06924
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Targeted protein degradation is largely performed by the ubiquitin-proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. It is currently unclear how the proteaso ...

    Targeted protein degradation is largely performed by the ubiquitin-proteasome pathway, in which substrate proteins are marked by covalently attached ubiquitin chains that mediate recognition by the proteasome. It is currently unclear how the proteasome recognizes its substrates, as the only established ubiquitin receptor intrinsic to the proteasome is Rpn10/S5a (ref. 1), which is not essential for ubiquitin-mediated protein degradation in budding yeast. In the accompanying manuscript we report that Rpn13 (refs 3-7), a component of the nine-subunit proteasome base, functions as a ubiquitin receptor, complementing its known role in docking de-ubiquitinating enzyme Uch37/UCHL5 (refs 4-6) to the proteasome. Here we merge crystallography and NMR data to describe the ubiquitin-binding mechanism of Rpn13. We determine the structure of Rpn13 alone and complexed with ubiquitin. The co-complex reveals a novel ubiquitin-binding mode in which loops rather than secondary structural elements are used to capture ubiquitin. Further support for the role of Rpn13 as a proteasomal ubiquitin receptor is demonstrated by its ability to bind ubiquitin and proteasome subunit Rpn2/S1 simultaneously. Finally, we provide a model structure of Rpn13 complexed to diubiquitin, which provides insights into how Rpn13 as a ubiquitin receptor is coupled to substrate deubiquitination by Uch37.


    Organizational Affiliation

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein ADRM1
A
153Mus musculusMutation(s): 0 
Gene Names: Adrm1 (Gp110)
Find proteins for Q9JKV1 (Mus musculus)
Go to UniProtKB:  Q9JKV1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.428α = 90.00
b = 56.223β = 90.00
c = 63.242γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
HKL-2000data collection
SHARPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance