1RGD

STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Submitted: 11 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.

van Tilborg, M.A.Bonvin, A.M.Hard, K.Davis, A.L.Maler, B.Boelens, R.Yamamoto, K.R.Kaptein, R.

(1995) J.Mol.Biol. 247: 689-700

  • DOI: 10.1006/jmbi.1995.0173

  • PubMed Abstract: 
  • The solution structure of the glucocorticoid receptor (GR) DNA-binding domain (DBD), consisting of 93 residues, has been refined from two and three-dimensional NMR data using an ensemble iterative relaxation matrix approach followed by direct NOE ref ...

    The solution structure of the glucocorticoid receptor (GR) DNA-binding domain (DBD), consisting of 93 residues, has been refined from two and three-dimensional NMR data using an ensemble iterative relaxation matrix approach followed by direct NOE refinement with DINOSAUR. A set of 47 structures of the rat GR fragment Cys440-Arg510 was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-up curves in H2O and 2H2O via relaxation matrix calculations (1186 distance constraints from NOE intensities, 10 phi and 22 chi 1 dihedral angle constraints from J- coupling data were used for the calculations). The root-mean-square deviation values of the 11 best structures on the well-determined part of the protein (Cys440 to Ser448, His451 to Glu469 and Pro493 to Glu508) are 0.60 A and 1.20 A from the average for backbone and all heavy atoms, respectively. The final structures have R-factors around 0.40 and good stereochemical qualities. The first zinc-coordinating domain of the GR DBD is very similar to the crystal structure with a root-mean-square difference of 1.4 A. The second zinc-coordinating domain is still disordered in solution. No secondary structure element is found in this domain in the free state. As suggested by crystallographic studies on the estrogen receptor DBD-DNA and GR DBD-DNA complexes, part of this region will form a distorted helix and the D-box will undergo a conformational change upon cooperative binding to DNA.


    Related Citations: 
    • Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA
      Luisi, B.F.,Xu, W.X.,Otwinowski, Z.,Freedman, L.P.,Yamamoto, K.R.,Sigler, P.B.
      (1991) Nature 352: 497
    • Solution Structure of the Glucocorticoid Receptor DNA-Binding Domain
      Hard, T.,Kellenbach, E.,Boelens, R.,Maler, B.A.,Dahlman, K.,Freedman, L.P.,Carlstedt-Duke, J.,Yamamoto, K.R.,Gustafsson, J.-A.,Kaptein, R.
      (1990) Science 249: 157
    • 1H NMR Studies of the Glucocorticoid Receptor DNA-Binding Domain: Sequential Assignments and Identification of Secondary Structure Elements
      Hard, T.,Kellenbach, E.,Boelens, R.,Kaptein, R.,Dahlman, K.,Carlstedt-Duke, J.,Freedman, L.P.,Maler, B.A.,Hyde, E.,Gustafsson, J.-A.,Yamamoto, K.R.
      (1990) Biochemistry 29: 9015


    Organizational Affiliation

    Bijvoet Center for Biomolecular Research Utrecht University, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUCOCORTICOID RECEPTOR
A
71Rattus norvegicusMutation(s): 0 
Gene Names: Nr3c1 (Grl)
Find proteins for P06536 (Rattus norvegicus)
Go to UniProtKB:  P06536
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Submitted: 11 
  • Olderado: 1RGD Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance