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

    Department of Molecular Genetics, University of Toronto, ON M5S 1A8, Canada.,Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada.,Cell Biology Program, Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; Department of Biochemistry, University of Toronto, ON M5S 1A8, Canada; Institute of Medical Science, University of Toronto, ON M5S 1A8, Canada.,Département de Biochimie, de Microbiologie et de Bio-informatique, PROTEO et IBIS, Université Laval, Québec City, QC G1V 0A6, Canada.,Department of Biochemistry, McGill University, Montreal, QC H3G 0B1, Canada.,Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada.,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.,Department of Biochemistry, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, 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



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