4F38

Crystal structure of geranylgeranylated RhoA in complex with RhoGDI in its active GPPNHP-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Quantitative Analysis of Prenylated RhoA Interaction with Its Chaperone, RhoGDI.

Tnimov, Z.Guo, Z.Gambin, Y.Nguyen, U.T.Wu, Y.W.Abankwa, D.Stigter, A.Collins, B.M.Waldmann, H.Goody, R.S.Alexandrov, K.

(2012) J Biol Chem 287: 26549-26562

  • DOI: https://doi.org/10.1074/jbc.M112.371294
  • Primary Citation of Related Structures:  
    4F38

  • PubMed Abstract: 

    Small GTPases of the Rho family regulate cytoskeleton remodeling, cell polarity, and transcription, as well as the cell cycle, in eukaryotic cells. Membrane delivery and recycling of the Rho GTPases is mediated by Rho GDP dissociation inhibitor (RhoGDI), which forms a stable complex with prenylated Rho GTPases. We analyzed the interaction of RhoGDI with the active and inactive forms of prenylated and unprenylated RhoA. We demonstrate that RhoGDI binds the prenylated form of RhoA·GDP with unexpectedly high affinity (K(d) = 5 pm). The very long half-life of the complex is reduced 25-fold on RhoA activation, with a concomitant reduction in affinity (K(d) = 3 nm). The 2.8-Å structure of the RhoA·guanosine 5'-[β,γ-imido] triphosphate (GMPPNP)·RhoGDI complex demonstrated that complex formation forces the activated RhoA into a GDP-bound conformation in the absence of nucleotide hydrolysis. We demonstrate that membrane extraction of Rho GTPase by RhoGDI is a thermodynamically favored passive process that operates through a series of progressively tighter intermediates, much like the one that is mediated by RabGDI.


  • Organizational Affiliation

    Department of Molecular Cell Biology, Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St. Lucia, Queensland 4072, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transforming protein RhoA195Mus musculusMutation(s): 0 
Gene Names: RhoaArhaArha2
EC: 3.6.5.2
UniProt
Find proteins for Q9QUI0 (Mus musculus)
Explore Q9QUI0 
Go to UniProtKB:  Q9QUI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QUI0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rho GDP-dissociation inhibitor 1204Mus musculusMutation(s): 0 
Gene Names: ArhgdiaC87222Gdi1
UniProt
Find proteins for Q99PT1 (Mus musculus)
Explore Q99PT1 
Go to UniProtKB:  Q99PT1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99PT1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46α = 90
b = 71.576β = 90
c = 136.03γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASESphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-08-15
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary