6E6H

NRAS G13D bound to GppNHp (N13GNP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D.

Johnson, C.W.Lin, Y.J.Reid, D.Parker, J.Pavlopoulos, S.Dischinger, P.Graveel, C.Aguirre, A.J.Steensma, M.Haigis, K.M.Mattos, C.

(2019) Cell Rep 28: 1538-1550.e7

  • DOI: 10.1016/j.celrep.2019.07.026
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ras GTPases are mutated at codons 12, 13, and 61, with different frequencies in KRas, HRas, and NRas and in a cancer-specific manner. The G13D mutant appears in 25% of KRas-driven colorectal cancers, while observed only rarely in HRas or NRas. Struct ...

    Ras GTPases are mutated at codons 12, 13, and 61, with different frequencies in KRas, HRas, and NRas and in a cancer-specific manner. The G13D mutant appears in 25% of KRas-driven colorectal cancers, while observed only rarely in HRas or NRas. Structures of Ras G13D in the three isoforms show an open active site, with adjustments to the D13 backbone torsion angles and with disconnected switch regions. KRas G13D has unique features that destabilize the nucleotide-binding pocket. In KRas G13D bound to GDP, A59 is placed in the Mg 2+ binding site, as in the HRas-SOS complex. Structure and biochemistry are consistent with an intermediate level of KRas G13D bound to GTP, relative to wild-type and KRas G12D, observed in genetically engineered mouse models. The results explain in part the elevated frequency of the G13D mutant in KRas over the other isoforms of Ras.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA. Electronic address: c.mattos@northeastern.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase NRas
A
166Homo sapiensMutation(s): 1 
Gene Names: NRASHRAS1
Find proteins for P01111 (Homo sapiens)
Go to UniProtKB:  P01111
NIH Common Fund Data Resources
PHAROS  P01111
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
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: 0.236 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.553α = 90
b = 39.565β = 106.4
c = 65.016γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesMCB-1517295

Revision History 

  • Version 1.0: 2019-07-31
    Type: Initial release
  • Version 1.1: 2019-09-04
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence