1rgd

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{{STRUCTURE_1rgd| PDB=1rgd | SCENE= }}
{{STRUCTURE_1rgd| PDB=1rgd | SCENE= }}
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'''STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS'''
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===STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS===
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==Overview==
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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.
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{{ABSTRACT_PUBMED_7723024}}
==About this Structure==
==About this Structure==
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1RGD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RGD OCA].
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1RGD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RGD OCA].
==Reference==
==Reference==
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[[Category: Yamamoto, K R.]]
[[Category: Yamamoto, K R.]]
[[Category: Dna-binding protein]]
[[Category: Dna-binding protein]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 07:27:56 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 19:36:49 2008''

Revision as of 16:36, 28 July 2008

Image:1rgd.png

Template:STRUCTURE 1rgd

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

Template:ABSTRACT PUBMED 7723024

About this Structure

1RGD is a Single protein structure of sequence from Rattus norvegicus. Full experimental information is available from OCA.

Reference

Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations., van Tilborg MA, Bonvin AM, Hard K, Davis AL, Maler B, Boelens R, Yamamoto KR, Kaptein R, J Mol Biol. 1995 Apr 7;247(4):689-700. PMID:7723024

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