5CQ9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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; Department of Molecular Genetics, University of Toronto, ON M5S 1A8, Canada; Institute of Medical Science, University of Toronto, ON M5S 1A8, Canada; Sickkids IBD Centre, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada. Electronic address: john.brumell@sickkids.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Secreted effector protein sopD2
A, B
319Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 0 
Gene Names: sopD2STM0972
Find proteins for Q8ZQC8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZQC8
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
11-mer peptide
C, D
11Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 0 
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.309 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.239 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.613α = 90
b = 89.8β = 117.15
c = 75.595γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaGSP-48370

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-09-16
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence