Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 38764.26 
• Atom Count: 2420 
• Residue Count: 345 
• Unique protein chains: 2

4DID

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

• DOI: 10.2210/pdb4DID/pdb

• Classification: HYDROLASE/HYDROLASE
• Organism(s): Homo sapiens, Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
• Expression System: Escherichia coli BL21(DE3)


• 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: 2.3501 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 

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: 10.1074/jbc.M111.331330


• 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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cell division control protein 42 homolog	A	193	Homo sapiens	Mutation(s): 0  Gene Names: CDC42
Find proteins for P60953 (Homo sapiens) Go to Gene View: CDC42 Go to UniProtKB:  P60953

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

Small Molecules

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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GDP	Kd: 6000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3501 Å
• R-Value Free: 0.237 
• R-Value Work: 0.207 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 106.880	α = 90.00
b = 106.880	β = 90.00
c = 87.570	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-30 
• 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
  Type: Database references
• Version 1.2: 2012-05-02
  Type: Database references