PDBsum entry 1rgd

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protein metals links
DNA-binding protein PDB id
Protein chain
71 a.a. *
_ZN ×2
* Residue conservation analysis
PDB id:
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
06-Jan-95     Release date:   14-Feb-95    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06536  (GCR_RAT) -  Glucocorticoid receptor
795 a.a.
71 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     regulation of transcription, DNA-dependent   1 term 
  Biochemical function     DNA binding     5 terms  


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.
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, 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.  
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