4XKH

CRYSTAL STRUCTURE OF THE AIRAPL TANDEM UIMS IN COMPLEX WITH A LYS48-LINKED TRI-UBIQUITIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Selective Binding of AIRAPL Tandem UIMs to Lys48-Linked Tri-Ubiquitin Chains.

Rahighi, S.Braunstein, I.Ternette, N.Kessler, B.Kawasaki, M.Kato, R.Matsui, T.Weiss, T.M.Stanhill, A.Wakatsuki, S.

(2016) Structure 24: 412-422

  • DOI: 10.1016/j.str.2015.12.017

  • PubMed Abstract: 
  • Lys48-linked ubiquitin chains act as the main targeting signals for protein degradation by the proteasome. Here we report selective binding of AIRAPL, a protein that associates with the proteasome upon exposure to arsenite, to Lys48-linked tri-ubiqui ...

    Lys48-linked ubiquitin chains act as the main targeting signals for protein degradation by the proteasome. Here we report selective binding of AIRAPL, a protein that associates with the proteasome upon exposure to arsenite, to Lys48-linked tri-ubiquitin chains. AIRAPL comprises two ubiquitin-interacting motifs in tandem (tUIMs) that are linked through a flexible inter-UIM region. In the complex crystal structure UIM1 binds the proximal ubiquitin, whereas UIM2 (the double-sided UIM) binds non-symmetrically to the middle and distal ubiquitin moieties on either side of the helix. Specificity of AIRAPL for Lys48-linked ubiquitin chains is determined by UIM2, and the flexible inter-UIM linker increases avidity by placing the two UIMs in an orientation that facilitates binding of the third ubiquitin to UIM1. Unlike middle and proximal ubiquitins, distal ubiquitin binds UIM2 through a novel surface, which leaves the Ile44 hydrophobic patch accessible for binding to the proteasomal ubiquitin receptors.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-C
A, F, B, D, G, I
76Bos taurusGene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to Gene View: UBC
Go to UniProtKB:  P0CH28
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AN1-type zinc finger protein 2B
E, C, H
55Mus musculusGene Names: Zfand2b (Airapl)
Find proteins for Q91X58 (Mus musculus)
Go to UniProtKB:  Q91X58
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 90.860α = 90.00
b = 90.860β = 90.00
c = 61.010γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-03-09
    Type: Database references