3A1Q

Crystal structure of the mouse RAP80 UIMs in complex with Lys63-linked di-ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80

Sato, Y.Yoshikawa, A.Mimura, H.Yamashita, M.Yamagata, A.Fukai, S.

(2009) Embo J. 28: 2461-2468

  • DOI: 10.1038/emboj.2009.160

  • PubMed Abstract: 
  • RAP80 has a key role in the recruitment of the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA-damage foci for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs (UIMs). Here, we r ...

    RAP80 has a key role in the recruitment of the Abraxas-BRCC36-BRCA1-BARD1 complex to DNA-damage foci for DNA repair through specific recognition of Lys 63-linked polyubiquitinated proteins by its tandem ubiquitin-interacting motifs (UIMs). Here, we report the crystal structure of the RAP80 tandem UIMs (RAP80-UIM1-UIM2) in complex with Lys 63-linked di-ubiquitin at 2.2 A resolution. The two UIMs, UIM1 and UIM2, and the alpha-helical inter-UIM region together form a continuous 60 A-long alpha-helix. UIM1 and UIM2 bind to the proximal and distal ubiquitin moieties, respectively. Both UIM1 and UIM2 of RAP80 recognize an Ile 44-centered hydrophobic patch on ubiquitin but neither UIM interacts with the Lys 63-linked isopeptide bond. Our structure suggests that the inter-UIM region forms a 12 A-long alpha-helix that ensures that the UIMs are arranged to enable specific binding of Lys 63-linked di-ubiquitin. This was confirmed by pull-down analyses using RAP80-UIM1-UIM2 mutants of various length inter-UIM regions. Further, we show that the Epsin1 tandem UIM, which has an inter-UIM region similar to that of RAP80-UIM1-UIM2, also selectively binds Lys 63-linked di-ubiquitin.


    Organizational Affiliation

    Structural Biology Laboratory, Life Science Division, Synchrotron Radiation Research Organization and Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, D
77Mus musculusMutation(s): 1 
Gene Names: Ubc
Find proteins for P0CG50 (Mus musculus)
Go to UniProtKB:  P0CG50
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
B, E
76Mus musculusMutation(s): 1 
Gene Names: Ubc
Find proteins for P0CG50 (Mus musculus)
Go to UniProtKB:  P0CG50
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin interaction motif-containing protein 1
C, F
45Mus musculusMutation(s): 0 
Gene Names: Uimc1 (Rap80, Rip110, Rxrip110)
Find proteins for Q5U5Q9 (Mus musculus)
Go to UniProtKB:  Q5U5Q9
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.235α = 90.00
b = 74.810β = 90.00
c = 83.031γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
HKL-2000data reduction
ADSCdata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance