8S1O | pdb_00008s1o

Crystal structure of human Rac1-GDP-Pi


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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Literature

The cytokinesis regulator RacGAP1 is a Rac1-specific GAP on membranes.

Dubois, P.Ferrandez, Y.Rey, C.Pages, C.Nawrotek, A.Cherfils, J.

(2026) Protein Sci 35: e70488-e70488

  • DOI: https://doi.org/10.1002/pro.70488
  • Primary Citation Related Structures: 
    8S1N, 8S1O

  • PubMed Abstract: 

    Rho family small GTPases are essential for cytokinesis completion. RacGAP1, a dimeric multidomain protein with a lipid-binding C1 domain and a GTPase-activating protein (GAP) domain, is a major regulator in this process. However, despite many cellular and biochemical studies, whether RhoA or Rac1 is the actual substrate inactivated by RacGAP1 has remained a matter of debate. Rho family GTPases are inactivated by their GAPs on membranes, but the activity and specificity of RacGAP1 have only been studied biochemically in solution. Here, we reconstituted RacGAP1 in a membrane environment, using liposomes and highly purified proteins. Our study reveals that PS is a major lipid required for RacGAP1 membrane-binding in addition to PIP 2 , and that the GAP domain cooperates with the C1 domain for membrane-binding. Consistently, fluorescence-based kinetics show that membranes potentiate the activity of RacGAP1 and of the C1GAP and GAP constructs towards Rac1. However, membranes do not modify RacGAP1 marked specificity for Rac1, identifying it as a Rac1-selective GAP. The Rac1-GDP-Pi crystal structure and mutagenesis identify the switch 1 and the insert region as important determinants for this specificity. Together, our results suggest a structural model in which the Rac1-RacGAP1 complex associates snugly with the membrane to efficiently remove Rac1 from the division plane.


  • Organizational Affiliation
    • CNRS, Ecole Normale Superieure Paris-Saclay, Université Paris-Saclay, Gif-sur-Yvette, France.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related C3 botulinum toxin substrate 1177Homo sapiensMutation(s): 0 
Gene Names: RAC1TC25MIG5
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
GTEx:  ENSG00000136238 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63000
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.209 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.32α = 90
b = 89.58β = 90
c = 108.68γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXrefinement
autoPROCdata processing
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Database references