Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28605.54 
• Atom Count: 1922 
• Residue Count: 244 
• Unique protein chains: 2

4G0N

Crystal Structure of wt H-Ras-GppNHp bound to the RBD of Raf Kinase

• DOI: 10.2210/pdb4G0N/pdb

• Classification: PROTEIN BINDING/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2012-07-09 Released: 2013-07-17 
• Deposition Author(s): Fetics, S.K., Kearney, B.M., Buhrman, G., Mattos, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 

Literature

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD.

Fetics, S.K., Guterres, H., Kearney, B.M., Buhrman, G., Ma, B., Nussinov, R., Mattos, C.

(2015) Structure 23: 505-516

• PubMed: 25684575 
• DOI: 10.1016/j.str.2014.12.017
• Primary Citation of Related Structures:  
  4G3X


• PubMed Abstract: 
  

The Ras/Raf/MEK/ERK signal transduction pathway is a major regulator of cell proliferation activated by Ras-guanosine triphosphate (GTP). The oncogenic mutant RasQ61L is not able to hydrolyze GTP in the presence of Raf and thus is a constitutive activator of this mitogenic pathway. The Ras/Raf interaction is essential for the activation of the Raf kinase domain through a currently unknown mechanism. We present the crystal structures of the Ras-GppNHp/Raf-RBD and RasQ61L-GppNHp/Raf-RBD complexes, which, in combination with MD simulations, reveal differences in allosteric interactions leading from the Ras/Raf interface to the Ras calcium-binding site and to the remote Raf-RBD loop L4. In the presence of Raf, the RasQ61L mutant has a rigid switch II relative to the wild-type and increased flexibility at the interface with switch I, which propagates across Raf-RBD. We show that in addition to local perturbations on Ras, RasQ61L has substantial long-range effects on the Ras allosteric lobe and on Raf-RBD.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
GTPase HRas	A	166	Homo sapiens	Mutation(s): 0  Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens) Go to Gene View: HRAS Go to UniProtKB:  P01112

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
RAF proto-oncogene serine/threonine-protein kinase	B	78	Homo sapiens	Mutation(s): 0  Gene Names: RAF1 (RAF) EC: 2.7.11.1
Find proteins for P04049 (Homo sapiens) Go to Gene View: RAF1 Go to UniProtKB:  P04049

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
DTU	A	(2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL C4 H10 O2 S2 VHJLVAABSRFDPM-ZXZARUISSA-N
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GNP	A	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 0.229 
• R-Value Work: 0.181 
• Space Group: P 3 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 90.440	α = 90.00
b = 90.440	β = 90.00
c = 92.703	γ = 120.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing
PHENIX	refinement
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-07-09 
• Released Date: 2013-07-17 
• Deposition Author(s): Fetics, S.K., Kearney, B.M., Buhrman, G., Mattos, C.

Revision History 

• Version 1.0: 2013-07-17
  Type: Initial release
• Version 1.1: 2015-03-11
  Type: Database references