3W31

Structual basis for the recognition of Ubc13 by the Shigella flexneri effector OspI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.245 

Starting Models: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural basis for the recognition of Ubc13 by the Shigella flexneri effector OspI.

Nishide, A.Kim, M.Takagi, K.Himeno, A.Sanada, T.Sasakawa, C.Mizushima, T.

(2013) J Mol Biol 425: 2623-2631

  • DOI: https://doi.org/10.1016/j.jmb.2013.02.037
  • Primary Citation of Related Structures:  
    3W30, 3W31

  • PubMed Abstract: 

    Ubc13 is a ubiquitin-conjugating enzyme that plays a key role in the nuclear factor-κB signal transduction pathway in human diseases. The Shigella flexneri effector OspI affects inflammatory responses by catalyzing the deamidation of a specific glutamine residue at position 100 in Ubc13 during infection. This modification prevents the activation of the TNF (tumor necrosis factor) receptor-associated factor 6, leading to modulation of the diacylglycerol-CBM (CARD-Bcl10-Malt1) complex-TNF receptor-associated factor 6-nuclear factor-κB signaling pathway. To elucidate the structural basis of OspI function, we determined the crystal structures of the catalytically inert OspI C62A mutant and its complex with Ubc13 at resolutions of 3.0 and 2.96Å, respectively. The structure of the OspI-Ubc13 complex revealed that the interacting surfaces between OspI and Ubc13 are a hydrophobic surface and a complementary charged surface. Furthermore, we predict that the complementary charged surface of OspI plays a key role in substrate specificity determination.


  • Organizational Affiliation

    Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF169b220Shigella flexneriMutation(s): 1 
Gene Names: ORF169bCP0209
UniProt
Find proteins for Q8VSD5 (Shigella flexneri)
Explore Q8VSD5 
Go to UniProtKB:  Q8VSD5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8VSD5
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 N155Homo sapiensMutation(s): 0 
Gene Names: UBE2NBLU
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens)
Explore P61088 
Go to UniProtKB:  P61088
PHAROS:  P61088
GTEx:  ENSG00000177889 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61088
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.96 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.245 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.238α = 90
b = 119.238β = 90
c = 69.985γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description