Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.65 kDa 
• Atom Count: 3922 
• Residue Count: 486 
• Unique protein chains: 2

1WQ1

RAS-RASGAP COMPLEX

• DOI: 10.2210/pdb1WQ1/pdb

• Classification: COMPLEX (GTP-BINDING/GTPASE ACTIVATION)
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-07-03 Released: 1998-07-15 
• Deposition Author(s): Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmueller, L., Lautwein, A., Schmitz, F., Wittinghofer, A.

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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 

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: 9219684 
• 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 2.5 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-RAS	R	166	Homo sapiens	Mutation(s): 0  Gene Names: H-RAS-1, HRAS, HRAS1 EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS  P01112 GTEx  ENSG00000174775

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
P120GAP	G	334	Homo sapiens	Mutation(s): 0  Gene Names: GENE FRAGMENT OF P120GAP POSI, RASA1, GAP, RASA
Find proteins for P20936 (Homo sapiens) Explore P20936  Go to UniProtKB:  P20936
NIH Common Fund Data Resources
PHAROS  P20936 GTEx  ENSG00000145715

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	R	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
AF3	R	ALUMINUM FLUORIDE Al F3 KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG	R	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 71.9	α = 90
b = 41.1	β = 108.4
c = 89	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XSCALE	data scaling
X-PLOR	model building
X-PLOR	refinement
XDS	data reduction
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-07-03 
• Released Date: 1998-07-15 
Deposition Author(s): Scheffzek, K., Ahmadian, M.R., Kabsch, W., Wiesmueller, L., Lautwein, A., Schmitz, F., Wittinghofer, A.

Revision History 

• 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