Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19571.82 
• Atom Count: 1418 
• Residue Count: 166 
• Unique protein chains: 1

1GNR

X-RAY CRYSTAL STRUCTURE ANALYSIS OF THE CATALYTIC DOMAIN OF THE ONCOGENE PRODUCT P21H-RAS COMPLEXED WITH CAGED GTP AND MANT DGPPNHP

• DOI: 10.2210/pdb1GNR/pdb

• Classification: GTP BINDING PROTEIN
• Organism(s): Homo sapiens


• Deposited: 1995-05-11 Released: 1995-07-31 
• Deposition Author(s): Scheidig, A., Franken, S.M., Corrie, J.E.T., Reid, G.P., Wittinghofer, A., Pai, E.F., Goody, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.257 
• R-Value Work: 0.206 

Literature

X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp.

Scheidig, A.J., Franken, S.M., Corrie, J.E., Reid, G.P., Wittinghofer, A., Pai, E.F., Goody, R.S.

(1995) J.Mol.Biol. 253: 132-150

• PubMed: 7473708 
• DOI: 10.1006/jmbi.1995.0541
• Primary Citation of Related Structures:  
  1GNQ, 1GNP


• PubMed Abstract: 
  

The X-ray structures of the 1:1 complexes formed between p21H-ras (residues 1 to 166) and the nucleotides P3-1-(2-nitrophenyl)ethyl guanosine triphosphate ("caged GTP"; pure R- and S-diastereomers) and 3'-O-(N-methylanthraniloyl)-2'-deoxyguanosine 5'-(beta, gamma-imido)-triphosphate ("mant dG-ppNHp"), have been refined to an R-factor of 21.4% (R-caged GTP, 1.85 A resolution), 18.9% (S-caged GTP, 2.5 A resolution) and 17.6% (mant dGppNHp, 2.7 A resolution), respectively. Details of the structure determination, refinement and the structures themselves are presented. The overall structures of the complexes are identical in terms of the general organization of their secondary structure elements and are also identical to that reported for the analogous complex of p21H-ras with GppNHp. The binding of the GTP part is not significantly affected by the additional aromatic group (cage and mant, respectively) in contrast to the original observation on p21:caged GTP using the racemic mixture of R- and S-caged GTP. The main differences in the structures are observed in the region of loop L2 (residues Glu31 to Thr35) where the additional aromatic group attached to the nucleotide comes very close to the side-chain of Tyr32, including backbone displacements of 2.6 A, 2.2 A and 0.3 A for the residues from Glu31 to Thr35 for R-caged, S-caged GTP and mant dGppNHp, respectively. The refined structures provide additional data for the design of new nucleotide analogs and the importance of their stereochemistry as well as for the design of new mutant forms of p21H-ras for further biochemical investigations. The binding mode of mant dGppNHp reveals significant features for the understanding of the fluorescence signals observed in solution.

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Related Citations: 

• Crystallographic Studies on P21H-Ras Using Synchrotron Laue Method: Improvement of Crystal Quality and Monitoring of the Gtpase Reaction at Different Time Points
  Scheidig, A.J.,Sanchez-Llorente, A.,Lautwein, A.,Pai, E.F.,Corrie, J.E.T.,Reid, G.P.,Wittinghofer, A.,Goody, R.S.
  (1994) Acta Crystallogr.,Sect.D 50: 512




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Organizational Affiliation: 

Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-H-RAS P21 PROTEIN	A	166	Homo sapiens	Mutation(s): 0  Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens) Go to Gene View: HRAS Go to UniProtKB:  P01112

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CAG	A	GUANOSINE 5'-TRIPHOSPHATE P3-[1-(2-NITROPHENYL)ETHYL ESTER] C18 H23 N6 O16 P3 NYWDUFBXCCSYMK-JPDTYCKISA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.257 
• R-Value Work: 0.206 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 40.400	α = 90.00
b = 40.400	β = 90.00
c = 158.800	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-05-11 
• Released Date: 1995-07-31 
• Deposition Author(s): Scheidig, A., Franken, S.M., Corrie, J.E.T., Reid, G.P., Wittinghofer, A., Pai, E.F., Goody, R.S.

Revision History 

• Version 1.0: 1995-07-31
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance