4DID

Crystal structure of Salmonella effector N-terminal domain SopB in complex with Cdc42

• PDB DOI: https://doi.org/10.2210/pdb4DID/pdb

• Classification: HYDROLASE/HYDROLASE
• Organism(s): Homo sapiens, Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-01-30 Released: 2012-02-29 
• Deposition Author(s): Burkinshaw, B.J., Strynadka, N.C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Structure of Salmonella Effector Protein SopB N-terminal Domain in Complex with Host Rho GTPase Cdc42.

Burkinshaw, B.J., Prehna, G., Worrall, L.J., Strynadka, N.C.

(2012) J Biol Chem 287: 13348-13355

• PubMed: 22362774 
• DOI: https://doi.org/10.1074/jbc.M111.331330
• Primary Citation of Related Structures:  
  4DID


• PubMed Abstract: 
  

  SopB is a type III secreted Salmonella effector protein with phosphoinositide phosphatase activity and a distinct GTPase binding domain. The latter interacts with host Cdc42, an essential Rho GTPase that regulates critical events in eukaryotic cytoskeleton organization and membrane trafficking. Structural and biochemical analysis of the SopB GTPase binding domain in complex with Cdc42 shows for the first time that SopB structurally and functionally mimics a host guanine nucleotide dissociation inhibitor (GDI) by contacting key residues in the regulatory switch regions of Cdc42 and slowing Cdc42 nucleotide exchange.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology and Center for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 38.76 kDa 
• Atom Count: 2,491 
• Modelled Residue Count: 306 
• Deposited Residue Count: 345 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 42 homolog	A	193	Homo sapiens	Mutation(s): 0  Gene Names: CDC42 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens) Explore P60953  Go to UniProtKB:  P60953
PHAROS:  P60953 GTEx:  ENSG00000070831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Inositol phosphate phosphatase sopB	B	152	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0  Gene Names: sigD, sopB, STM1091 EC: 3.1.3
UniProt
Find proteins for O30916 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore O30916  Go to UniProtKB:  O30916

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.88	α = 90
b = 106.88	β = 90
c = 87.57	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Burkinshaw, B.J., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2012-03-14
  Changes: Database references
• Version 1.2: 2012-05-02
  Changes: Database references
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description