5CPC | pdb_00005cpc

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

• PDB DOI: https://doi.org/10.2210/pdb5CPC/pdb

• Classification: CELL INVASION
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-21 Released: 2015-09-09 
• Deposition Author(s): Shi, R., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
• Funding Organization(s): Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

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

• PubMed: 26299973 
• DOI: https://doi.org/10.1016/j.celrep.2015.07.063
• Primary Citation Related Structures: 
  5CPC, 5CQ9


• 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 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.

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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.
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.
Department of Biochemistry, McGill University, Montreal, QC H3G 0B1, Canada; Department of Biochemistry, University of Saskatchewan, Saskatoon, SK S7N 5E5, 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.
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: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.38 kDa 
• Atom Count: 4,585 
• Modeled Residue Count: 561 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Secreted effector protein SopD	A, B	317	Salmonella enterica subsp. enterica serovar Typhimurium str. LT2	Mutation(s): 0  Gene Names: sopD, STM2945
UniProt
Find proteins for P40722 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P40722  Go to UniProtKB:  P40722

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.243 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.525	α = 90
b = 102.743	β = 105.53
c = 76.018	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Shi, R., Cygler, M., Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	GSP-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
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references