1RGD

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

Summary for 1RGD

• Entry DOI: 10.2210/pdb1rgd/pdb
• Descriptor: GLUCOCORTICOID RECEPTOR, ZINC ION (2 entities in total)
• Functional Keywords: dna-binding protein, dna binding protein
• Biological source: Rattus norvegicus (Norway rat)
• Cellular location: Cytoplasm (By similarity): P06536
• Total number of polymer chains: 1
• Total formula weight: 8093.16

Authors

Van Tilborg, M.A.A.,Bonvin, A.M.J.J.,Hard, K.,Davis, A.,Maler, B.,Boelens, R.,Yamamoto, K.R.,Kaptein, R. (deposition date: 1995-01-06, release date: 1995-02-14, Last modification date: 2024-05-22)

Primary citation

van Tilborg, M.A.,Bonvin, A.M.,Hard, K.,Davis, A.L.,Maler, B.,Boelens, R.,Yamamoto, K.R.,Kaptein, R.
Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.
J.Mol.Biol., 247:689-700, 1995

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. 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.

PubMed: 7723024
DOI: 10.1006/jmbi.1995.0173

Experimental method

SOLUTION NMR