Biological Assembly 1  

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

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

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

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 40.09 kDa 
• Atom Count: 2861 
• Modelled Residue Count: 352 
• Deposited Residue Count: 352 
• Unique protein chains: 1

5N6O

Wild type human Rac1-GDP

• PDB DOI: 10.2210/pdb5N6O/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-02-15 Released: 2017-12-27 
• Deposition Author(s): Cherfils, J., Ferrandez, Y.
• Funding Organization(s): Labex lermit

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.252 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 

Literature

Allosteric inhibition of the guanine nucleotide exchange factor DOCK5 by a small molecule.

Ferrandez, Y., Zhang, W., Peurois, F., Akendengue, L., Blangy, A., Zeghouf, M., Cherfils, J.

(2017) Sci Rep 7: 14409-14409

• PubMed: 29089502 
• DOI: 10.1038/s41598-017-13619-2
• Primary Citation of Related Structures:  
  5N6O


• PubMed Abstract: 
  

Rac small GTPases and their GEFs of the DOCK family are pivotal checkpoints in development, autoimmunity and bone homeostasis, and their abnormal regulation is associated to diverse pathologies. Small molecules that inhibit their activities are therefore needed to investigate their functions. Here, we characterized the mechanism of inhibition of human DOCK5 by C21, a small molecule that inhibits mouse Dock5 in cells and blocks bone degradation in mice models of osteoporosis. We showed that the catalytic DHR2 domain of DOCK5 has a high basal GEF activity in the absence of membranes which is not regulated by a simple feedback loop. C21 blocks this activity in a non-competitive manner and is specific for DOCK5. In contrast, another Dock inhibitor, CPYPP, inhibits both DOCK5 and an unrelated GEF, Trio. To gain insight into structural features of the inhibitory mechanism of C21, we used SAXS analysis of DOCK5 ^DHR2 and crystallographic analysis of unbound Rac1-GDP. Together, these data suggest that C21 takes advantage of intramolecular dynamics of DOCK5 and Rac1 to remodel the complex into an unproductive conformation. Based on this allosteric mechanism, we propose that diversion of intramolecular dynamics is a potent mechanism for the inhibition of multidomain regulators of small GTPases.

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Organizational Affiliation: 

Laboratoire de Biologie et Pharmacologie Appliquée, CNRS and Ecole Normale Supérieure Paris-Saclay, Cachan, France. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related C3 botulinum toxin substrate 1	A, B	176	Homo sapiens	Mutation(s): 0  Gene Names: RAC1, TC25, MIG5 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P63000 (Homo sapiens) Explore P63000  Go to UniProtKB:  P63000
PHAROS:  P63000

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.252 
• R-Value Work: 0.193 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.641	α = 90
b = 82.656	β = 90
c = 105.898	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
BUSTER	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-02-15 
• Released Date: 2017-12-27 
Deposition Author(s): Cherfils, J., Ferrandez, Y.

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Funding Organization	Location	Grant Number
Labex lermit	France	--

Revision History  

• Version 1.0: 2017-12-27
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2019-10-16
  Changes: Data collection
• Version 1.3: 2020-11-18
  Changes: Derived calculations, Structure summary