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 1.3 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
  • Primary Citation of Related Structures:  
    1RGD

  • 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 refinement with DINOSAUR ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOCORTICOID RECEPTORA71Rattus norvegicusMutation(s): 0 
Gene Names: Nr3c1Grl
UniProt
Find proteins for P06536 (Rattus norvegicus)
Explore P06536 
Go to UniProtKB:  P06536
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06536
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth 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




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Database references, Derived calculations, Other, Structure summary