1HH4

Rac1-RhoGDI complex involved in NADPH oxidase activation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.256 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Crystal Structure of the Rac1-Rhogdi Complex Involved in Nadph Oxidase Activation

Grizot, S., Faure, J., Fieschi, F., Vignais, P.V., Dagher, M.-C., Pebay-Peyroula, E.

(2001) Biochemistry 40: 10007


  • PubMed Abstract: 

    • A heterodimer of prenylated Rac1 and Rho GDP dissociation inhibitor was purified and found to be competent in NADPH oxidase activation. Small angle neutron scattering experiments confirmed a 1:1 stoichiometry. The crystal structure of the Rac1-RhoGDI ...

    A heterodimer of prenylated Rac1 and Rho GDP dissociation inhibitor was purified and found to be competent in NADPH oxidase activation. Small angle neutron scattering experiments confirmed a 1:1 stoichiometry. The crystal structure of the Rac1-RhoGDI complex was determined at 2.7 A resolution. In this complex in which Rac1 is bound to GDP, the switch I region of Rac1 is in the GDP conformation whereas the switch II region resembles that of a GTP-bound GTPase. Two types of interaction between RhoGTPases and RhoGDI were investigated. The lipid-protein interaction between the geranylgeranyl moiety of Rac1 and RhoGDI resulted in numerous structural changes in the core of RhoGDI. The interactions between Rac1 and RhoGDI occur through hydrogen bonds which involve a number of residues of Rac1, namely, Tyr64(Rac), Arg66(Rac), His103(Rac), and His104(Rac), conserved within the Rho family and localized in the switch II region or in its close neighborhood. Moreover, in the switch II region of Rac1, hydrophobic interactions involving Leu67(Rac) and Leu70(Rac) contribute to the stability of the Rac1-RhoGDI complex. Inhibition of the GDP-GTP exchange in Rac1 upon binding to RhoGDI partly results from interaction of Thr35(Rac) with Asp45(GDI). In the Rac1-RhoGDI complex, the accessibility of the effector loops of Rac1 probably accounts for the ability of the Rac1-RhoGDI complex to activate the NADPH oxidase.

    Organizational Affiliation: 

    Institut de Biologie Structurale, CEA-CNRS-UJF, UMR 5075, 41 Rue Jules Horowitz, 38027 Grenoble Cedex 1, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
A, B
192Homo sapiensMutation(s): 0 
Gene Names: RAC1 (TC25)
EC: 3.6.5.2
Find proteins for P63000 (Homo sapiens)
Go to Gene View: RAC1
Go to UniProtKB:  P63000
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RHO GDP-DISSOCIATION INHIBITOR 1
D, E
204Homo sapiensMutation(s): 0 
Gene Names: ARHGDIA (GDIA1)
Find proteins for P52565 (Homo sapiens)
Go to Gene View: ARHGDIA
Go to UniProtKB:  P52565
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GER
Query on GER
Download SDF File 
Download CCD File 
D, E
GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.256 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 154.700α = 90.00
b = 88.700β = 90.00
c = 62.600γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
AMoREphasing
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-05-08
    Type: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-05-15
    Type: Data collection, Experimental preparation