1rgd
From Proteopedia
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|PDB= 1rgd |SIZE=350|CAPTION= <scene name='initialview01'>1rgd</scene> | |PDB= 1rgd |SIZE=350|CAPTION= <scene name='initialview01'>1rgd</scene> | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene> | + | |LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rgd OCA], [http://www.ebi.ac.uk/pdbsum/1rgd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rgd RCSB]</span> | ||
}} | }} | ||
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[[Category: Tilborg, M A.A Van.]] | [[Category: Tilborg, M A.A Van.]] | ||
[[Category: Yamamoto, K R.]] | [[Category: Yamamoto, K R.]] | ||
| - | [[Category: ZN]] | ||
[[Category: dna-binding protein]] | [[Category: dna-binding protein]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:27:48 2008'' |
Revision as of 20:27, 30 March 2008
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| Ligands: | |||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE REFINEMENT OF THE GLUCOCORTICOID RECEPTOR-DNA BINDING DOMAIN FROM NMR DATA BY RELAXATION MATRIX CALCULATIONS
Overview
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.
About this Structure
1RGD is a Single protein structure of sequence from Rattus norvegicus. Full crystallographic 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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