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.

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

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
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.

Organizational Affiliation

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

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens) Explore P60953 Go to UniProtKB: P60953
PHAROS: P60953 GTEx: ENSG00000070831
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60953
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O30916
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
GDP	Binding MOAD: 4DID	Kd: 6000 (nM) from 1 assay(s)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-02-29

Deposition Author(s):

Burkinshaw, B.J.

Strynadka, N.C.J.

Revision History (Full details and data files)

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