Crystal Structure of a GDP-bound G12V Oncogenic Mutant of Human GTPase KRas

Experimental Data Snapshot

  • Resolution: 1.49 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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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

  • DOI: https://doi.org/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. Biochemical profiling and subclassification of KRAS-driven cancers will enable the rational selection of therapies targeting specific KRAS isoforms or specific RAS effectors.

  • Organizational Affiliation

    Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
GTPase KRas
A, B
169Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens)
Explore P01116 
Go to UniProtKB:  P01116
PHAROS:  P01116
GTEx:  ENSG00000133703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.32α = 90
b = 41.427β = 105.09
c = 115.119γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-10
    Type: Initial release
  • Version 1.1: 2015-06-17
    Changes: Database references
  • Version 1.2: 2015-09-30
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.4: 2023-12-27
    Changes: Data collection, Database references, Derived calculations