Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 27.94 kDa 
• Atom Count: 2103 
• Residue Count: 237 
• Unique protein chains: 1

2IJE

Crystal Structure of the Cdc25 domain of RasGRF1

• DOI: 10.2210/pdb2IJE/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-09-29 Released: 2006-10-31 
• Deposition Author(s): Freedman, T.S., Kuriyan, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.205 

Literature

A Ras-induced conformational switch in the Ras activator Son of sevenless.

Freedman, T.S., Sondermann, H., Friedland, G.D., Kortemme, T., Bar-Sagi, D., Marqusee, S., Kuriyan, J.

(2006) Proc Natl Acad Sci U S A 103: 16692-16697

• PubMed: 17075039 
• DOI: 10.1073/pnas.0608127103
• Primary Citation of Related Structures:  
  2II0, 2IJE


• PubMed Abstract: 
  

The Ras-specific guanine nucleotide-exchange factors Son of sevenless (Sos) and Ras guanine nucleotide-releasing factor 1 (RasGRF1) transduce extracellular stimuli into Ras activation by catalyzing the exchange of Ras-bound GDP for GTP. A truncated form of RasGRF1 containing only the core catalytic Cdc25 domain is sufficient for stimulating Ras nucleotide exchange, whereas the isolated Cdc25 domain of Sos is inactive. At a site distal to the catalytic site, nucleotide-bound Ras binds to Sos, making contacts with the Cdc25 domain and with a Ras exchanger motif (Rem) domain. This allosteric Ras binding stimulates nucleotide exchange by Sos, but the mechanism by which this stimulation occurs has not been defined. We present a crystal structure of the Rem and Cdc25 domains of Sos determined at 2.0-A resolution in the absence of Ras. Differences between this structure and that of Sos bound to two Ras molecules show that allosteric activation of Sos by Ras occurs through a rotation of the Rem domain that is coupled to a rotation of a helical hairpin at the Sos catalytic site. This motion relieves steric occlusion of the catalytic site, allowing substrate Ras binding and nucleotide exchange. A structure of the isolated RasGRF1 Cdc25 domain determined at 2.2-A resolution, combined with computational analyses, suggests that the Cdc25 domain of RasGRF1 is able to maintain an active conformation in isolation because the helical hairpin has strengthened interactions with the Cdc25 domain core. These results indicate that RasGRF1 lacks the allosteric activation switch that is crucial for Sos activity.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, California Institute for Quantitative Biomedical Research, University of California, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-releasing protein	S	240	Mus musculus	Mutation(s): 0  Gene Names: 19417, Rasgrf1, Cdc25, Grf1
Find proteins for P27671 (Mus musculus) Explore P27671  Go to UniProtKB:  P27671
NIH Common Fund Data Resources
IMPC:  MGI:99694

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	S	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.242 
• R-Value Work: 0.200 
• R-Value Observed: 0.205 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.43	α = 90
b = 77.801	β = 90
c = 110.303	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-29 
• Released Date: 2006-10-31 
Deposition Author(s): Freedman, T.S., Kuriyan, J.

Revision History 

• Version 1.0: 2006-10-31
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2014-04-30
  Changes: Data collection