1WQ1

RAS-RASGAP COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.233 
  • R-Value Observed: 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

  • DOI: 10.1126/science.277.5324.333
  • Primary Citation of Related Structures:  
    1WQ1

  • 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 fluoride was solved at a resolution of 2 ...

    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: 
    • The Interaction of Ras with Gtpase-Activating Proteins
      Wittinghofer, A., Scheffzek, K., Ahmadian, M.R.
      (1997) FEBS Lett 410: 63
    • 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
    • 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
    • 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
    • Biological and Biochemical Properties of Human Rash Genes Mutated at Codon 61
      Der, C.J., Finkel, T., Cooper, G.M.
      (1986) Cell 44: 167
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
H-RASA [auth R]166Homo sapiensMutation(s): 0 
Gene Names: H-RAS-1HRASHRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
P120GAPB [auth G]334Homo sapiensMutation(s): 0 
Gene Names: GENE FRAGMENT OF P120GAP POSIRASA1GAPRASA
Find proteins for P20936 (Homo sapiens)
Explore P20936 
Go to UniProtKB:  P20936
NIH Common Fund Data Resources
PHAROS:  P20936
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
D [auth R]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
AF3
Query on AF3

Download Ideal Coordinates CCD File 
E [auth R]ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.9α = 90
b = 41.1β = 108.4
c = 89γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XSCALEdata scaling
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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