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 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transforming protein RhoAA195Mus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rho GDP-dissociation inhibitor 1B204Mus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
GER
Query on GER

Download Ideal Coordinates CCD File 
C [auth A]GERAN-8-YL GERAN
C20 H34
HSOYJGBJQAKCNA-CAIKYXSQSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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