1WQ1

RAS-RASGAP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Ras-RasGAP complex: structural basis for GTPase activation and its loss in oncogenic Ras mutants.

Scheffzek, K.Ahmadian, M.R.Kabsch, W.Wiesmuller, L.Lautwein, A.Schmitz, F.Wittinghofer, A.

(1997) Science 277: 333-338


  • PubMed Abstract: 
  • The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluorid ...

    The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.


    Related Citations: 
    • Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 A Resolution: Implications for the Mechanism of GTP Hydrolysis
      Pai, E.F.,Krengel, U.,Petsko, G.A.,Goody, R.S.,Kabsch, W.,Wittinghofer, A.
      (1990) Embo J. 9: 2351
    • A Cytoplasmic Protein Stimulates Normal N-Ras P21 Gtpase, But Does not Affect Oncogenic Mutants
      Trahey, M.,Mccormick, F.
      (1987) Science 238: 542
    • Formation of a Transition-State Analog of the Ras Gtpase Reaction by Ras-Gdp, Tetrafluoroaluminate, and Gtpase-Activating Proteins
      Mittal, R.,Ahmadian, M.R.,Goody, R.S.,Wittinghofer, A.
      (1996) Science 273: 115
    • Biological Properties of Human C-Ha-Ras1 Genes Mutated at Codon 12
      Seeburg, P.H.,Colby, W.W.,Capon, D.J.,Goeddel, D.V.,Levinson, A.D.
      (1984) Nature 312: 71
    • Crystal Structure of the Gtpase-Activating Domain of Human P120Gap and Implications for the Interaction with Ras
      Scheffzek, K.,Lautwein, A.,Kabsch, W.,Ahmadian, M.R.,Wittinghofer, A.
      (1996) Nature 384: 591
    • The Interaction of Ras with Gtpase-Activating Proteins
      Wittinghofer, A.,Scheffzek, K.,Ahmadian, M.R.
      (1997) FEBS Lett. 410: 63
    • Biological and Biochemical Properties of Human Rash Genes Mutated at Codon 61
      Der, C.J.,Finkel, T.,Cooper, G.M.
      (1986) Cell 44: 167


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Abteilung Strukturelle Biologie, Rheinlanddamm 201, 44139 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-RAS
R
166Homo sapiensMutation(s): 0 
Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
P120GAP
G
334Homo sapiensMutation(s): 0 
Gene Names: RASA1 (GAP, RASA)
Find proteins for P20936 (Homo sapiens)
Go to Gene View: RASA1
Go to UniProtKB:  P20936
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

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

Download SDF File 
Download CCD File 
R
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
AF3
Query on AF3

Download SDF File 
Download CCD File 
R
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.900α = 90.00
b = 41.100β = 108.40
c = 89.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
XSCALEdata scaling
X-PLORrefinement
X-PLORmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-07-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance