2NTX

Prone8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Evidence for a Common Intermediate in Small G Protein-GEF Reactions

Thomas, C., Fricke, I., Scrima, A., Berken, A., Wittinghofer, A.

(2007) Mol Cell 25: 141-149

  • DOI: 10.1016/j.molcel.2006.11.023
  • Primary Citation of Related Structures:  
    2NTX, 2NTY

  • PubMed Abstract: 

    • Rho of plants (Rop) proteins belong to the superfamily of small GTP-binding (G) proteins and are vital regulators of signal transduction in plants. In order to become activated, Rop proteins need to exchange GDP for GTP, an intrinsically slow process catalyzed by guanine nucleotide exchange factors (GEFs) ...

    Rho of plants (Rop) proteins belong to the superfamily of small GTP-binding (G) proteins and are vital regulators of signal transduction in plants. In order to become activated, Rop proteins need to exchange GDP for GTP, an intrinsically slow process catalyzed by guanine nucleotide exchange factors (GEFs). RopGEFs show no homology to animal RhoGEFs, and the catalytic mechanism remains elusive. GEF-catalysed nucleotide exchange proceeds via transient ternary and stable binary complexes. While a number of structural studies have analyzed binary nucleotide-free G protein-GEF complexes, very little is known about the ternary complexes. Here we report the X-ray structure of the catalytic PRONE domain of RopGEF8 from Arabidopsis thaliana, both alone and in a ternary complex with Rop4 and GDP. The features of the latter complex, a transient intermediate of the exchange reaction never directly observed before, suggest a common mechanism of catalyzed nucleotide exchange applicable to small G proteins in general.

    Related Citations: 
    • Purification and crystallization of the catalytic PRONE domain of RopGEF8 and its complex with Rop4 from Arabidopsis thaliana
      Thomas, C., Weyand, M., Wittinghofer, A., Berken, A.
      (2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 607
    Organizational Affiliation: 

    Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Emb|CAB41934.1A, B365Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g24620, ROPGEF8, MOB24.21
UniProt
Find proteins for Q9LV40 (Arabidopsis thaliana)
Explore Q9LV40 
Go to UniProtKB:  Q9LV40
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LV40
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.339α = 90
b = 114.339β = 90
c = 318.964γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SHARPphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance