Biological Assembly 1  

 3D View: Structure | Electron Density

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 84345.79 
• Atom Count: 4675 
• Residue Count: 730 
• Unique protein chains: 1

2NTX

Prone8

• DOI: 10.2210/pdb2NTX/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli


• Deposited: 2006-11-08 Released: 2007-01-23 
• Deposition Author(s): Thomas, C., Fricke, I., Scrima, A., Berken, A., Wittinghofer, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.270 
• R-Value Work: 0.244 

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

• PubMed: 17218277 
• DOI: 10.1016/j.molcel.2006.11.023
• Primary Citation of Related Structures:  
  2NTY
• Also Cited By: 2WBL


• 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). 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.

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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 62: 607




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Emb|CAB41934.1	A, B	365	Arabidopsis thaliana	Mutation(s): 0  Gene Names: ROPGEF8
Find proteins for Q9LV40 (Arabidopsis thaliana) Go to UniProtKB:  Q9LV40

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.270 
• R-Value Work: 0.244 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 114.339	α = 90.00
b = 114.339	β = 90.00
c = 318.964	γ = 120.00

Software Package:

Software Name	Purpose
SHARP	phasing
RESOLVE	phasing
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-08 
• Released Date: 2007-01-23 
• Deposition Author(s): Thomas, C., Fricke, I., Scrima, A., Berken, A., Wittinghofer, A.

Revision History 

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