4XKH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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
  • Primary Citation of Related Structures:  
    4XKH

  • 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-ubiquitin chains ...

    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; Structural Molecular Biology, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Photon Science, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA. Electronic address: soichi.wakatsuki@stanford.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-CA, D [auth B], F [auth D], C [auth F], G, I76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Explore P0CH28 
Go to UniProtKB:  P0CH28
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AN1-type zinc finger protein 2BE [auth C], B [auth E], H55Mus musculusMutation(s): 0 
Gene Names: Zfand2bAirapl
Find proteins for Q91X58 (Mus musculus)
Explore Q91X58 
Go to UniProtKB:  Q91X58
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.86α = 90
b = 90.86β = 90
c = 61.01γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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