Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.33 kDa 
• Atom Count: 1475 
• Modelled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

1LF5

Crystal Structure of RasA59G in the GDP-bound Form

• PDB DOI: 10.2210/pdb1LF5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2002-04-10 Released: 2002-11-06 
• Deposition Author(s): Hall, B.E., Bar-Sagi, D., Nassar, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.222 

Literature

The Structural Basis for the Transition from Ras-GTP to Ras-GDP

Hall, B.E., Bar-Sagi, D., Nassar, N.

(2002) Proc Natl Acad Sci U S A 99: 12138-12142

• PubMed: 12213964 
• DOI: 10.1073/pnas.192453199
• Primary Citation of Related Structures:  
  1LF0, 1LF5


• PubMed Abstract: 
  

The conformational changes in Ras that accompany the hydrolysis of GTP are critical to its function as a molecular switch in signaling pathways. Understanding how GTP is hydrolyzed by revealing the sequence of intermediary structures in the reaction is essential for understanding Ras signaling. Until now, no structure of an intermediate in GTP hydrolysis has been experimentally determined for Ras alone. We have solved the crystal structure of the Ala-59 to Gly mutant of Ras, (RasA59G), bound to guanosine 5'-imidotriphosphate or GDP to 1.7-A resolution. In the guanosine 5'-imidotriphosphate-bound form, this mutant adopts a conformation that is intermediate between the GTP- and GDP-bound forms of wild-type Ras and that is similar to what has been predicted by molecular dynamics simulation [Ma, J. P. & Karplus, M. (1997) Proc. Natl. Acad. Sci. USA 94, 11905-11910]. This conformation is stabilized by direct and water-mediated interactions between the switch 1 and switch 2 regions and is characterized by an increase in the binding affinity for GTP. We propose that the structural changes promoted by the Ala-59 to Gly mutation exhibit a discrete conformational state assumed by wild-type Ras during GTP hydrolysis.

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Organizational Affiliation: 

Graduate Program in Molecular and Cellular Pharmacology, Department of Molecular Genetics, Stony Brook University, Stony Brook, NY 11794-8661, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transforming protein P21/H-RAS-1	A	166	Homo sapiens	Mutation(s): 1  Gene Names: HRAS, HRAS1 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.245 
• R-Value Work: 0.222 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.112	α = 90
b = 93.112	β = 90
c = 120.301	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-04-10 
• Released Date: 2002-11-06 
Deposition Author(s): Hall, B.E., Bar-Sagi, D., Nassar, N.

Revision History  

• Version 1.0: 2002-11-06
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 2.0: 2021-10-27
  Changes: Atomic model, Database references, Derived calculations