Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 19.90 kDa 
• Atom Count: 1638 
• Modelled Residue Count: 170 
• Deposited Residue Count: 170 
• Unique protein chains: 1

4QL3

Crystal Structure of a GDP-bound G12R Oncogenic Mutant of Human GTPase KRas

• PDB DOI: 10.2210/pdb4QL3/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2014-06-10 Released: 2015-06-10 
• Deposition Author(s): Hunter, J.C., Manandhar, A., Gurbani, D., Chen, Z., Westover, K.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.162 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 

Literature

Biochemical and Structural Analysis of Common Cancer-Associated KRAS Mutations.

Hunter, J.C., Manandhar, A., Carrasco, M.A., Gurbani, D., Gondi, S., Westover, K.D.

(2015) Mol Cancer Res 13: 1325-1335

• PubMed: 26037647 
• DOI: 10.1158/1541-7786.MCR-15-0203
• Primary Citation of Related Structures:  
  4QL3, 4TQ9, 4TQA, 4WA7


• PubMed Abstract: 
  

KRAS mutations are the most common genetic abnormalities in cancer, but the distribution of specific mutations across cancers and the differential responses of patients with specific KRAS mutations in therapeutic clinical trials suggest that different KRAS mutations have unique biochemical behaviors. To further explain these high-level clinical differences and to explore potential therapeutic strategies for specific KRAS isoforms, we characterized the most common KRAS mutants biochemically for substrate binding kinetics, intrinsic and GTPase-activating protein (GAP)-stimulated GTPase activities, and interactions with the RAS effector, RAF kinase. Of note, KRAS G13D shows rapid nucleotide exchange kinetics compared with other mutants analyzed. This property can be explained by changes in the electrostatic charge distribution of the active site induced by the G13D mutation as shown by X-ray crystallography. High-resolution X-ray structures are also provided for the GDP-bound forms of KRAS G12V, G12R, and Q61L and reveal additional insight. Overall, the structural data and measurements, obtained herein, indicate that measurable biochemical properties provide clues for identifying KRAS-driven tumors that preferentially signal through RAF.

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Organizational Affiliation: 

Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	A	170	Homo sapiens	Mutation(s): 1  Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Explore P01116  Go to UniProtKB:  P01116
PHAROS:  P01116

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.04 Å
• R-Value Free: 0.162 
• R-Value Work: 0.138 
• R-Value Observed: 0.139 
• Space Group: P 2₁ 2₁ 2₁
• Diffraction Data DOI: 10.15785/SBGRID/160 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.125	α = 90
b = 40.908	β = 90
c = 91.806	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-10 
• Released Date: 2015-06-10 
Deposition Author(s): Hunter, J.C., Manandhar, A., Gurbani, D., Chen, Z., Westover, K.D.

Revision History  

• Version 1.0: 2015-06-10
  Type: Initial release
  
• Version 1.1: 2015-09-02
  Changes: Database references
• Version 1.2: 2015-09-30
  Changes: Database references