Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.07 kDa 
• Atom Count: 2703 
• Residue Count: 344 
• Unique protein chains: 2

3W31

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

• DOI: 10.2210/pdb3W31/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Shigella flexneri, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-12-07 Released: 2013-03-27 
• Deposition Author(s): Nishide, A., Kim, M., Takagi, K., Sasakawa, C., Mizushima, T.

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Experimental Data Snapshot

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

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 

• PubMed: 23542009 
• DOI: 10.1016/j.jmb.2013.02.037
• Structures With Same Primary Citation


• 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
ORF169b	A	220	Shigella flexneri	Mutation(s): 1  Gene Names: ORF169b, CP0209, SF_p0209
Find proteins for Q8VSD5 (Shigella flexneri) Explore Q8VSD5  Go to UniProtKB:  Q8VSD5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-conjugating enzyme E2 N	B	155	Homo sapiens	Mutation(s): 0  Gene Names: UBE2N, BLU EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt)
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
NIH Common Fund Data Resources
PHAROS  P61088 GTEx  ENSG00000177889

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	A, B	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

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 = 119.238	α = 90
b = 119.238	β = 90
c = 69.985	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-12-07 
• Released Date: 2013-03-27 
Deposition Author(s): Nishide, A., Kim, M., Takagi, K., Sasakawa, C., Mizushima, T.

Revision History 

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2013-07-17
  Changes: Database references