Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.30 kDa 
• Atom Count: 1437 
• Modelled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

1ZVQ

Structure of the Q61G mutant of Ras in the GDP-bound form

• DOI: 10.2210/pdb1ZVQ/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-06-02 Released: 2006-03-14 
• Deposition Author(s): Ford, B., Nassar, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Structure of a transient intermediate for GTP hydrolysis by ras.

Ford, B., Hornak, V., Kleinman, H., Nassar, N.

(2006) Structure 14: 427-436

• PubMed: 16531227 
• DOI: 10.1016/j.str.2005.12.010
• Primary Citation of Related Structures:  
  1ZVQ, 1ZW6


• PubMed Abstract: 
  

The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals a new conformation of switch 2 that bears remarkable structural homology to an intermediate for GTP hydrolysis revealed by targeted molecular dynamics simulations. The mutation increased retention of GTP and inhibited Ras binding to the catalytic site, but not to the distal site of Sos. Most importantly, the thermodynamics of RafRBD binding to Ras are altered even though the structure of switch 1 is not affected by the mutation. Our results suggest that interplay and transmission of structural information between the switch regions are important factors for Ras function. They propose that initiation of GTP hydrolysis sets off the separation of the Ras/effector complex even before the GDP conformation is reached.

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Related Citations: 

• 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

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Organizational Affiliation: 

Department of Physiology and Biophysics, Basic Sciences Tower, Stony Brook University, Stony Brook, New York 11794, 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
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112 GTEx:  ENSG00000174775

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.229 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.992	α = 90
b = 92.992	β = 90
c = 121.015	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-02 
• Released Date: 2006-03-14 
Deposition Author(s): Ford, B., Nassar, N.

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Advisory, Refinement description