5WHD

Crystal structure of KRas G12V/D38P, bound to GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.641 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Exceptionally high-affinity Ras binders that remodel its effector domain.

McGee, J.H.Shim, S.Y.Lee, S.J.Swanson, P.K.Jiang, S.Y.Durney, M.A.Verdine, G.L.

(2018) J. Biol. Chem. 293: 3265-3280

  • DOI: 10.1074/jbc.M117.816348
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ras proteins are aberrantly activated in a wide range of human cancers, often endowing tumors with aggressive properties and resistance to therapy. Decades of effort to develop direct Ras inhibitors for clinical use have thus far failed, largely ...

    The Ras proteins are aberrantly activated in a wide range of human cancers, often endowing tumors with aggressive properties and resistance to therapy. Decades of effort to develop direct Ras inhibitors for clinical use have thus far failed, largely because of a lack of adequate small-molecule-binding pockets on the Ras surface. Here, we report the discovery of Ras-binding miniproteins from a naïve library and their evolution to afford versions with midpicomolar affinity to Ras. A series of biochemical experiments indicated that these miniproteins bind to the Ras effector domain as dimers, and high-resolution crystal structures revealed that these miniprotein dimers bind Ras in an unprecedented mode in which the Ras effector domain is remodeled to expose an extended pocket that connects two isolated pockets previously found to engage small-molecule ligands. We also report a Ras point mutant that stabilizes the protein in the open conformation trapped by these miniproteins. These findings provide new tools for studying Ras structure and function and present opportunities for the development of both miniprotein and small-molecule inhibitors that directly target the Ras proteins.


    Organizational Affiliation

    FOG Pharmaceuticals, Cambridge, Massachusetts 02140.,From the Departments of Molecular and Cellular Biology, gregory_verdine@harvard.edu.,From the Departments of Molecular and Cellular Biology.,Chemistry and Chemical Biology, Harvard University and Harvard Medical School, Cambridge, Massachusetts 02138 and.,Stem Cell and Regenerative Biology, and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase KRas
A, B, C, D
170Homo sapiensMutation(s): 2 
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, C, D
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.641 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.239α = 90.00
b = 80.912β = 90.62
c = 108.041γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LustgartenUnited States--

Revision History 

  • Version 1.0: 2018-01-03
    Type: Initial release
  • Version 1.1: 2018-01-10
    Type: Database references
  • Version 1.2: 2018-03-14
    Type: Database references