4WA7

Crystal Structure of a GDP-bound Q61L Oncogenic Mutant of Human GT- Pase KRas

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 


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

  • 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 ...

    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.

    Organizational Affiliation: 

    Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. kenneth.westover@utsouthwestern.edu.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase KRasA170Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01116
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.188 
  • Space Group: P 63
  • Diffraction Data DOI: 10.15785/SBGRID/161 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.493α = 90
b = 82.493β = 90
c = 40.761γ = 120
Software Package:
Software NamePurpose
HKL-3000data collection
HKL-2000data reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2015-09-23
    Changes: Database references
  • Version 1.3: 2017-11-22
    Changes: Derived calculations, Refinement description