5CQ9

Crystal structure of SopD2, a type III secreted virulence effector from Salmonella enterica

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Salmonella Disrupts Host Endocytic Trafficking by SopD2-Mediated Inhibition of Rab7.

D'Costa, V.M., Braun, V., Landekic, M., Shi, R., Proteau, A., McDonald, L., Cygler, M., Grinstein, S., Brumell, J.H.

(2015) Cell Rep 12: 1508-1518

  • DOI: 10.1016/j.celrep.2015.07.063
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Intracellular bacterial pathogens of a diverse nature share the ability to evade host immunity by impairing trafficking of endocytic cargo to lysosomes for degradation, a process that is poorly understood. Here, we show that the Salmonella enterica t ...

    Intracellular bacterial pathogens of a diverse nature share the ability to evade host immunity by impairing trafficking of endocytic cargo to lysosomes for degradation, a process that is poorly understood. Here, we show that the Salmonella enterica type 3 secreted effector SopD2 mediates this process by binding the host regulatory GTPase Rab7 and inhibiting its nucleotide exchange. Consequently, this limits Rab7 interaction with its dynein- and kinesin-binding effectors RILP and FYCO1 and thereby disrupts host-driven regulation of microtubule motors. Our study identifies a bacterial effector capable of directly binding and thereby modulating Rab7 activity and a mechanism of endocytic trafficking disruption that may provide insight into the pathogenesis of other bacteria. Additionally, we provide a powerful tool for the study of Rab7 function, and a potential therapeutic target.

    Organizational Affiliation: 

    Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Secreted effector protein sopD2
A, B
319Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: sopD2
Find proteins for Q8ZQC8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZQC8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
11-mer peptide
C, D
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C, D
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.613α = 90.00
b = 89.800β = 117.15
c = 75.595γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaGSP-48370

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence, Derived calculations