4XH9 | pdb_00004xh9

CRYSTAL STRUCTURE OF HUMAN RHOA IN COMPLEX WITH DH/PH FRAGMENT OF THE GUANINE NUCLEOTIDE EXCHANGE FACTOR NET1

• PDB DOI: https://doi.org/10.2210/pdb4XH9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli DH1
• Mutation(s): Yes 


• Deposited: 2015-01-05 Released: 2015-01-14 
• Deposition Author(s): Garcia, C., Petit, P., Boutin, J.A., Ferry, G., Vuillard, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

A structural study of the complex between neuroepithelial cell transforming gene 1 (Net1) and RhoA reveals a potential anticancer drug hot spot.

Petit, A.P., Garcia-Petit, C., Bueren-Calabuig, J.A., Vuillard, L.M., Ferry, G., Boutin, J.A.

(2018) J Biological Chem 293: 9064-9077

• PubMed: 29695506 
• DOI: https://doi.org/10.1074/jbc.RA117.001123
• Primary Citation Related Structures: 
  4XH9


• PubMed Abstract: 
  

  The GTPase RhoA is a major player in many different regulatory pathways. RhoA catalyzes GTP hydrolysis, and its catalysis is accelerated when RhoA forms heterodimers with proteins of the guanine nucleotide exchange factor (GEF) family. Neuroepithelial cell transforming gene 1 (Net1) is a RhoA-interacting GEF implicated in cancer, but the structural features supporting the RhoA/Net1 interaction are unknown. Taking advantage of a simple production and purification process, here we solved the structure of a RhoA/Net1 heterodimer with X-ray crystallography at 2-Å resolution. Using a panel of several techniques, including molecular dynamics simulations, we characterized the RhoA/Net1 interface. Moreover, deploying an extremely simple peptide-based scanning approach, we found that short peptides (penta- to nonapeptides) derived from the protein/protein interaction region of RhoA could disrupt the RhoA/Net1 interaction and thereby diminish the rate of nucleotide exchange. The most inhibitory peptide, EVKHF, spanning residues 102-106 in the RhoA sequence, displayed an IC ₅₀ of ∼100 μm without further modifications. The peptides identified here could be useful in further investigations of the RhoA/Net1 interaction region. We propose that our structural and functional insights might inform chemical approaches for transforming the pentapeptide into an optimized pseudopeptide that antagonizes Net1-mediated RhoA activation with therapeutic anticancer potential.

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Organizational Affiliation: 
• From the Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery and.
Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom and.
Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France.
Pôle d'Expertise Biotechnologie, Chimie, Biologie, Institut de Recherches SERVIER, 78290 Croissy-sur-Seine, France [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 125.04 kDa 
• Atom Count: 9,206 
• Modeled Residue Count: 1,022 
• Deposited Residue Count: 1,082 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuroepithelial cell-transforming gene 1 protein	A, C [auth D]	361	Homo sapiens	Mutation(s): 0  Gene Names: NET1, ARHGEF8
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z628 (Homo sapiens) Explore Q7Z628  Go to UniProtKB:  Q7Z628
PHAROS:  Q7Z628 GTEx:  ENSG00000173848

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein RhoA	B, D [auth E]	180	Homo sapiens	Mutation(s): 1  Gene Names: RHOA, ARH12, ARHA, RHO12 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P61586 (Homo sapiens) Explore P61586  Go to UniProtKB:  P61586
PHAROS:  P61586 GTEx:  ENSG00000067560

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.1	α = 90
b = 101.4	β = 94.3
c = 116.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Garcia, C., Petit, P., Boutin, J.A., Ferry, G., Vuillard, L.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2018-06-20
  Changes: Data collection, Database references
• Version 1.2: 2019-06-12
  Changes: Data collection, Structure summary
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description