1CRQ

THE SOLUTION STRUCTURE AND DYNAMICS OF RAS P21. GDP DETERMINED BY HETERONUCLEAR THREE AND FOUR DIMENSIONAL NMR SPECTROSCOPY


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure and dynamics of ras p21.GDP determined by heteronuclear three- and four-dimensional NMR spectroscopy.

Kraulis, P.J.Domaille, P.J.Campbell-Burk, S.L.Van Aken, T.Laue, E.D.

(1994) Biochemistry 33: 3515-3531

  • Primary Citation of Related Structures:  1CRP, 1CRR

  • PubMed Abstract: 
  • A high-resolution solution structure of the GDP form of a truncated version of the ras p21 protein (residues 1-166) has been determined using NMR spectroscopy. Ras p21 is the product of the human ras protooncogene and a member of a ubiquitous eukaryo ...

    A high-resolution solution structure of the GDP form of a truncated version of the ras p21 protein (residues 1-166) has been determined using NMR spectroscopy. Ras p21 is the product of the human ras protooncogene and a member of a ubiquitous eukaryotic gene family which is highly conserved in evolution. A virtually complete assignment (13C, 15N, and 1H), including stereospecific assignments of 54 C beta methylene protons and 10 C gamma methyl protons of valine residues, was obtained by analysis of three- and four-dimensional (3D and 4D) heteronuclear NMR spectra using a newly developed 3D/4D version of the ANSIG software. A total of 40 converged structures were computed from 3369 experimental restraints consisting of 3,167 nuclear Overhauser effect (NOE) derived distances, 14 phi and 54 chi 1 torsion angle restraints, 109 hydrogen bond distance restraints, and an additional 25 restraints derived from literature data defining interactions between the GDP ligand, the magnesium ion, and the protein. The structure in the region of residues 58-66 (loop L4), and to a lesser degree residues 30-38 (loop L2), is ill-defined. Analysis of the dynamics of the backbone 15N nuclei in the protein showed that residues within the regions 58-66, 107-109, and, to a lesser degree, 30-38 are dynamically mobile on the nanosecond time scale. The root mean square (rms) deviations between the 40 solution structures and the mean atomic coordinates are 0.78 A for the backbone heavy atoms and 1.29 A for all non-hydrogen atoms if all residues (1-166) are included in the analysis. If residues 30-38 and residues 58-66 are excluded from the analysis, the rms deviations are reduced to 0.55 and 1.00 A, respectively. The structure was compared to the most highly refined X-ray crystal structure of ras p21.GDP (1-189) [Milburn, M. V., Tong, L., de Vos, A. M., BrĂ¼nger, A. T., Yamaizumi, Z., Nishimura, S., & Kim, S.-H. (1990) Science 24, 939-945]. The structures are very similar except in the regions found to be mobile by NMR spectroscopy. In addition, the second alpha-helix (helix-2) has a slightly different orientation. The rms deviation between the average of the solution structures and the X-ray crystal structure is 0.94 A for the backbone heavy atoms if residues 31-37 and residues 59-73 are excluded from the analysis.


    Related Citations: 
    • Sequential Assignment of the Backbone Nuclei (1H, 15N, and 13C) of C-H-Ras P21 (1-166).Gdp Using a Novel 4D NMR Strategy
      Campbell-Burk, S.L.,Domaille, P.J.,Starovasnik, M.A.,Boucher, W.,Laue, E.D.
      (1992) J.Biomol.NMR 2: 639


    Organizational Affiliation

    Department of Biochemistry, University of Cambridge, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-H-RAS P21 PROTEIN
A
166Homo sapiensGene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance