Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 71.65 kDa 
• Atom Count: 4751 
• Modelled Residue Count: 582 
• Deposited Residue Count: 618 
• Unique protein chains: 2

2WMN

Structure of the complex between DOCK9 and Cdc42-GDP.

• PDB DOI: 10.2210/pdb2WMN/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-02 Released: 2009-09-22 
• Deposition Author(s): Yang, J., Roe, S.M., Barford, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.276 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 

Literature

Activation of Rho Gtpases by Dock Exchange Factors is Mediated by a Nucleotide Sensor.

Yang, J., Zhang, Z., Roe, S.M., Marshall, C.J., Barford, D.

(2009) Science 325: 1398

• PubMed: 19745154 
• DOI: 10.1126/science.1174468
• Primary Citation of Related Structures:  
  2WM9, 2WMN, 2WMO


• PubMed Abstract: 
  

Activation of Rho guanosine triphosphatases (GTPases) to the guanine triphosphate (GTP)-bound state is a critical event in their regulation of the cytoskeleton and cell signaling. Members of the DOCK family of guanine nucleotide exchange factors (GEFs) are important activators of Rho GTPases, but the mechanism of activation by their catalytic DHR2 domain is unknown. Through structural analysis of DOCK9-Cdc42 complexes, we identify a nucleotide sensor within the alpha10 helix of the DHR2 domain that contributes to release of guanine diphosphate (GDP) and then to discharge of the activated GTP-bound Cdc42. Magnesium exclusion, a critical factor in promoting GDP release, is mediated by a conserved valine residue within this sensor, whereas binding of GTP-Mg2+ to the nucleotide-free complex results in magnesium-inducing displacement of the sensor to stimulate discharge of Cdc42-GTP. These studies identify an unusual mechanism of GDP release and define the complete GEF catalytic cycle from GDP dissociation followed by GTP binding and discharge of the activated GTPase.

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Organizational Affiliation: 

Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DEDICATOR OF CYTOKINESIS PROTEIN 9	A	428	Homo sapiens	Mutation(s): 0  Gene Names: DOCK9, KIAA1058, ZIZ1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZ29 (Homo sapiens) Explore Q9BZ29  Go to UniProtKB:  Q9BZ29
PHAROS:  Q9BZ29

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION CONTROL PROTEIN 42 HOMOLOG	B	190	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.39 Å
• R-Value Free: 0.276 
• R-Value Work: 0.220 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.05	α = 90
b = 88.472	β = 90
c = 90.12	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-02 
• Released Date: 2009-09-22 
Deposition Author(s): Yang, J., Roe, S.M., Barford, D.

Revision History  

• Version 1.0: 2009-09-22
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance