1CC0

CRYSTAL STRUCTURE OF THE RHOA.GDP-RHOGDI COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

How RhoGDI binds Rho.

Longenecker, K.Read, P.Derewenda, U.Dauter, Z.Liu, X.Garrard, S.Walker, L.Somlyo, A.V.Nakamoto, R.K.Somlyo, A.P.Derewenda, Z.S.

(1999) Acta Crystallogr.,Sect.D 55: 1503-1515


  • PubMed Abstract: 
  • Like all Rho (Ras homology) GTPases, RhoA functions as a molecular switch in cell signaling, alternating between GTP- and GDP-bound states, with its biologically inactive GDP-bound form maintained as a cytosolic complex with RhoGDI (guanine nucleotid ...

    Like all Rho (Ras homology) GTPases, RhoA functions as a molecular switch in cell signaling, alternating between GTP- and GDP-bound states, with its biologically inactive GDP-bound form maintained as a cytosolic complex with RhoGDI (guanine nucleotide-exchange inhibitor). The crystal structures of RhoA-GDP and of the C-terminal immunoglobulin-like domain of RhoGDI (residues 67-203) are known, but the mechanism by which the two proteins interact is not known. The functional human RhoA-RhoGDI complex has been expressed in yeast and crystallized (P6(5)22, unit-cell parameters a = b = 139, c = 253 A, two complexes in the asymmetric unit). Although diffraction from these crystals extends to 3.5 A and is highly anisotropic, the experimentally phased (MAD plus MIR) electron-density map was adequate to reveal the mutual disposition of the two molecules. The result was validated by molecular-replacement calculations when data were corrected for anisotropy. Furthermore, the N-terminus of RhoGDI (the region involved in inhibition of nucleotide exchange) can be identified in the electron-density map: it is bound to the switch I and switch II regions of RhoA, occluding an epitope which binds Dbl-like nucleotide-exchange factors. The entrance of the hydrophobic pocket of RhoGDI is 25 A from the last residue in the RhoA model, with its C-terminus oriented to accommodate the geranylgeranyl group without conformational change in RhoA.


    Related Citations: 
    • Crystal Structure of Rhoa-Gdp and its Functional Implications
      Wei, Y.,Zhang, Y.,Derewenda, U.,Liu, X.,Minor, W.,Nakamoto, R.K.,Somlyo, A.V.,Somlyo, A.P.,Derewenda, Z.S.
      (1997) Nat.Struct.Mol.Biol. 4: 699
    • C-Terminal Binding Domain of Rho Gdp-Dissociation Inhibitor Directs N-Terminal Inhibitory Peptide to Gtpases
      Gosser, Y.Q.,Nomanbhoy, T.K.,Aghazadeh, B.,Manor, D.,Combs, C.,Cerione, R.A.,Rosen, M.K.
      (1997) Nature 387: 814
    • Crystal Structure of Human Rhoa in a Dominantly Active Form Complexed with a GTP Analogue
      Ihara, K.,Muraguchi, S.,Kato, M.,Shimizu, T.,Shirakawa, M.,Kuroda, S.,Kaibuchi, K.,Hakoshima, T.
      (1998) J.Biol.Chem. 273: 9656
    • A Modulator of Rho Family G Proteins, Rhogdi, Binds These G Proteins Via an Immunoglobulin-Like Domain and a Flexible N-Terminal Arm
      Keep, N.H.,Barnes, M.,Barsukov, I.,Badii, R.,Lian, L.,Segal, A.W.,Moody, P.C.E.,Roberts, G.C.K.
      (1997) Structure 5: 623


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia Health Sciences Center, Charlottesville, VA 22906, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
transforming protein rhoA
A, C
190Homo sapiensGene Names: RHOA (ARH12, ARHA, RHO12)
Find proteins for P61586 (Homo sapiens)
Go to Gene View: RHOA
Go to UniProtKB:  P61586
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
rho GDP dissociation inhibitor alpha
E, F
204Homo sapiensGene Names: ARHGDIA (GDIA1)
Find proteins for P52565 (Homo sapiens)
Go to Gene View: ARHGDIA
Go to UniProtKB:  P52565
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, C
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5 Å
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.300α = 90.00
b = 139.300β = 90.00
c = 253.100γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4model building
CCP4phasing
SCALEPACKdata scaling
MLPHAREphasing
AMoREphasing
Omodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-07
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance