6BOF

Crystal structure of KRAS A146T-GDP demonstrating open switch 1 conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.112 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Tissue-Specific Oncogenic Activity of KRASA146T.

Poulin, E.J.Bera, A.K.Lu, J.Lin, Y.J.Strasser, S.D.Paulo, J.A.Huang, T.Q.Morales, C.Yan, W.Cook, J.Nowak, J.A.Brubaker, D.K.Joughin, B.A.Johnson, C.W.DeStefanis, R.A.Ghazi, P.C.Gondi, S.Wales, T.E.Iacob, R.E.Bogdanova, L.Gierut, J.J.Li, Y.Engen, J.R.Perez-Mancera, P.A.Braun, B.S.Gygi, S.P.Lauffenburger, D.A.Westover, K.D.Haigis, K.M.

(2019) Cancer Discov 9: 738-755

  • DOI: 10.1158/2159-8290.CD-18-1220

  • PubMed Abstract: 
  • <i>KRAS </i> is the most frequently mutated oncogene. The incidence of specific <i>KRAS </i> alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS ...

    KRAS is the most frequently mutated oncogene. The incidence of specific KRAS alleles varies between cancers from different sites, but it is unclear whether allelic selection results from biological selection for specific mutant KRAS proteins. We used a cross-disciplinary approach to compare KRAS G12D , a common mutant form, and KRAS A146T , a mutant that occurs only in selected cancers. Biochemical and structural studies demonstrated that KRAS A146T exhibits a marked extension of switch 1 away from the protein body and nucleotide binding site, which activates KRAS by promoting a high rate of intrinsic and guanine nucleotide exchange factor-induced nucleotide exchange. Using mice genetically engineered to express either allele, we found that KRAS G12D and KRAS A146T exhibit distinct tissue-specific effects on homeostasis that mirror mutational frequencies in human cancers. These tissue-specific phenotypes result from allele-specific signaling properties, demonstrating that context-dependent variations in signaling downstream of different KRAS mutants drive the KRAS mutational pattern seen in cancer. SIGNIFICANCE: Although epidemiologic and clinical studies have suggested allele-specific behaviors for KRAS , experimental evidence for allele-specific biological properties is limited. We combined structural biology, mass spectrometry, and mouse modeling to demonstrate that the selection for specific KRAS mutants in human cancers from different tissues is due to their distinct signaling properties. See related commentary by Hobbs and Der, p. 696 . This article is highlighted in the In This Issue feature, p. 681 .


    Organizational Affiliation

    Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Harvard Digestive Disease Center, Harvard Medical School, Boston, Massachusetts.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Medicine, Harvard Medical School, Boston, Massachusetts.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts.,Department of Pediatrics and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas. khaigis@bidmc.harvard.edu Kenneth.Westover@UTSouthwestern.edu.,Department of Cell Biology, Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Department of Molecular and Clinical Cancer Medicine, Institute of Translational Medicine, University of Liverpool, Liverpool, UK.,Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, Massachusetts. khaigis@bidmc.harvard.edu Kenneth.Westover@UTSouthwestern.edu.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B
168Homo sapiensMutation(s): 1 
Gene Names: KRAS (KRAS2, RASK2)
Find proteins for P01116 (Homo sapiens)
Go to Gene View: KRAS
Go to UniProtKB:  P01116
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.401 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.112 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 78.024α = 90.00
b = 78.024β = 90.00
c = 55.863γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-19
    Type: Data collection, Database references, Structure summary