PDBsum entry 1rgd

DNA binding protein

PDB id

1rgd

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Contents

			Protein chain

					71 a.a. *

			Metals

					_ZN ×2

* Residue conservation analysis

PDB id:

1rgd

Links
- PDBe
- RCSB
- MMDB
- JenaLib
- Proteopedia
- CATH
- SCOP
- PDBSWS
- ProSAT

Name:

DNA binding protein

Title:

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

Structure:

Glucocorticoid receptor. Chain: a. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116

NMR struc:

11 models

Authors:

M.A.A.Van Tilborg,A.M.J.J.Bonvin,K.Hard,A.Davis,B.Maler,R.Boelens, K.R.Yamamoto,R.Kaptein

Key ref:

M.A.van Tilborg et al. (1995). Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations. J Mol Biol, 247, 689-700. PubMed id: 7723024

Date:

06-Jan-95

Release date:

14-Feb-95

PROCHECK

	Headers

	References

Protein chain

P06536 (GCR_RAT) - Glucocorticoid receptor from Rattus norvegicus

Seq: Struc:

Seq: Struc:					795 a.a. 71 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

	J Mol Biol 247:689-700 (1995)
PubMed id: 7723024

Structure refinement of the glucocorticoid receptor-DNA binding domain from NMR data by relaxation matrix calculations.
M.A.van Tilborg, A.M.Bonvin, K.Hård, A.L.Davis, B.Maler, R.Boelens, K.R.Yamamoto, R.Kaptein.

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.

Literature references that cite this PDB file's key reference

PubMed id

Reference

14592980

S.Devarakonda, J.M.Harp, Y.Kim, A.Ozyhar, and F.Rastinejad (2003).
Structure of the heterodimeric ecdysone receptor DNA-binding complex.

EMBO J, 22, 5827-5840.

PDB codes:

1r0n 1r0o

12211013

J.Bredenberg, and L.Nilsson (2002).
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.

Proteins, 49, 24-36.

10757981

M.Thompson, and N.W.Woodbury (2000).
Fluorescent and photochemical properties of a single zinc finger conjugated to a fluorescent DNA-binding probe.

Biochemistry, 39, 4327-4338.

10913286

P.J.van Tilborg, M.Czisch, F.A.Mulder, G.E.Folkers, A.M.Bonvin, M.Nair, R.Boelens, and R.Kaptein (2000).
Changes in dynamical behavior of the retinoid X receptor DNA-binding domain upon binding to a 14 base-pair DNA half site.

Biochemistry, 39, 8747-8757.

10026278

P.J.van Tilborg, F.A.Mulder, M.M.de Backer, M.Nair, E.C.van Heerde, G.Folkers, P.T.van der Saag, Y.Karimi-Nejad, R.Boelens, and R.Kaptein (1999).
Millisecond to microsecond time scale dynamics of the retinoid X and retinoic acid receptor DNA-binding domains and dimeric complex formation.

Biochemistry, 38, 1951-1956.

8995403

B.A.Lieberman, and S.K.Nordeen (1997).
DNA intersegment transfer, how steroid receptors search for a target site.

J Biol Chem, 272, 1061-1068.

9287161

H.Berglund, M.Wolf-Watz, T.Lundbäck, S.van den Berg, and T.Härd (1997).
Structure and dynamics of the glucocorticoid receptor DNA-binding domain: comparison of wild type and a mutant with altered specificity.

Biochemistry, 36, 11188-11197.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.