4G3X

Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.275 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD.

Fetics, S.K.Guterres, H.Kearney, B.M.Buhrman, G.Ma, B.Nussinov, R.Mattos, C.

(2015) Structure 23: 505-516

  • DOI: 10.1016/j.str.2014.12.017
  • Primary Citation of Related Structures:  
    4G0N, 4G3X

  • PubMed Abstract: 
  • The Ras/Raf/MEK/ERK signal transduction pathway is a major regulator of cell proliferation activated by Ras-guanosine triphosphate (GTP). The oncogenic mutant RasQ61L is not able to hydrolyze GTP in the presence of Raf and thus is a constitutive activator of this mitogenic pathway ...

    The Ras/Raf/MEK/ERK signal transduction pathway is a major regulator of cell proliferation activated by Ras-guanosine triphosphate (GTP). The oncogenic mutant RasQ61L is not able to hydrolyze GTP in the presence of Raf and thus is a constitutive activator of this mitogenic pathway. The Ras/Raf interaction is essential for the activation of the Raf kinase domain through a currently unknown mechanism. We present the crystal structures of the Ras-GppNHp/Raf-RBD and RasQ61L-GppNHp/Raf-RBD complexes, which, in combination with MD simulations, reveal differences in allosteric interactions leading from the Ras/Raf interface to the Ras calcium-binding site and to the remote Raf-RBD loop L4. In the presence of Raf, the RasQ61L mutant has a rigid switch II relative to the wild-type and increased flexibility at the interface with switch I, which propagates across Raf-RBD. We show that in addition to local perturbations on Ras, RasQ61L has substantial long-range effects on the Ras allosteric lobe and on Raf-RBD.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA. Electronic address: c.mattos@neu.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTPase HRasA166Homo sapiensMutation(s): 1 
Gene Names: HRASHRAS1
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
PHAROS:  P01112
GTEx:  ENSG00000174775 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01112
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAF proto-oncogene serine/threonine-protein kinaseB77Homo sapiensMutation(s): 0 
Gene Names: RAF1RAF
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens)
Explore P04049 
Go to UniProtKB:  P04049
PHAROS:  P04049
GTEx:  ENSG00000132155 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04049
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.275 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.4α = 90
b = 91.4β = 90
c = 93.11γ = 120
Software Package:
Software NamePurpose
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-17
    Type: Initial release
  • Version 1.1: 2015-03-11
    Changes: Database references
  • Version 1.2: 2015-03-18
    Changes: Derived calculations
  • Version 1.3: 2017-11-15
    Changes: Refinement description