1ZVQ

Structure of the Q61G mutant of Ras in the GDP-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of a transient intermediate for GTP hydrolysis by ras.

Ford, B.Hornak, V.Kleinman, H.Nassar, N.

(2006) Structure 14: 427-436

  • DOI: 10.1016/j.str.2005.12.010
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals ...

    The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals a new conformation of switch 2 that bears remarkable structural homology to an intermediate for GTP hydrolysis revealed by targeted molecular dynamics simulations. The mutation increased retention of GTP and inhibited Ras binding to the catalytic site, but not to the distal site of Sos. Most importantly, the thermodynamics of RafRBD binding to Ras are altered even though the structure of switch 1 is not affected by the mutation. Our results suggest that interplay and transmission of structural information between the switch regions are important factors for Ras function. They propose that initiation of GTP hydrolysis sets off the separation of the Ras/effector complex even before the GDP conformation is reached.


    Related Citations: 
    • The structural basis for the transition from Ras-GTP to Ras-GDP
      Hall, B.E.,Bar-Sagi, D.,Nassar, N.
      (2002) Proc.Natl.Acad.Sci.USA 99: 12138


    Organizational Affiliation

    Department of Physiology and Biophysics, Basic Sciences Tower, Stony Brook University, Stony Brook, New York 11794, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transforming protein p21/H-Ras-1
A
166Homo sapiensMutation(s): 1 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 92.992α = 90.00
b = 92.992β = 90.00
c = 121.015γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
REFMACrefinement
HKL-2000data reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-06-02 
  • Released Date: 2006-03-14 
  • Deposition Author(s): Ford, B., Nassar, N.

Revision History 

  • Version 1.0: 2006-03-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Advisory, Refinement description