5WDQ

H-Ras mutant L120A bound to GMP-PNP at 100K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.140 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Deconstruction of the Ras switching cycle through saturation mutagenesis.

Bandaru, P.Shah, N.H.Bhattacharyya, M.Barton, J.P.Kondo, Y.Cofsky, J.C.Gee, C.L.Chakraborty, A.K.Kortemme, T.Ranganathan, R.Kuriyan, J.

(2017) Elife 6: --

  • DOI: 10.7554/eLife.27810
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational to ...

    Ras proteins are highly conserved signaling molecules that exhibit regulated, nucleotide-dependent switching between active and inactive states. The high conservation of Ras requires mechanistic explanation, especially given the general mutational tolerance of proteins. Here, we use deep mutational scanning, biochemical analysis and molecular simulations to understand constraints on Ras sequence. Ras exhibits global sensitivity to mutation when regulated by a GTPase activating protein and a nucleotide exchange factor. Removing the regulators shifts the distribution of mutational effects to be largely neutral, and reveals hotspots of activating mutations in residues that restrain Ras dynamics and promote the inactive state. Evolutionary analysis, combined with structural and mutational data, argue that Ras has co-evolved with its regulators in the vertebrate lineage. Overall, our results show that sequence conservation in Ras depends strongly on the biochemical network in which it operates, providing a framework for understanding the origin of global selection pressures on proteins.


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, United States.,Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States.,Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Ragon Institute of MGH, MIT and Harvard, Cambridge, United States.,Department of Physics, Massachusetts Institute of Technology, Cambridge, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTPase HRas
A
170Homo 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 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

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Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.140 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 87.960α = 90.00
b = 87.960β = 90.00
c = 133.105γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesP01 AI091580
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Author supporting evidence