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PDBsum entry 1gdc
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protein metals links
Glucocorticoid receptor PDB id
1gdc

 

 

 

 

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Contents
Protein chain
72 a.a. *
Metals
_ZN ×2
* Residue conservation analysis
PDB id:
1gdc
Name: Glucocorticoid receptor
Title: Refined solution structure of the glucocorticoid receptor DNA-binding domain
Structure: Glucocorticoid receptor. Chain: a. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116
NMR struc: 1 models
Authors: H.Baumann,K.Paulsen,H.Kovacs,H.Berglund,A.P.H.Wright,J.-A.Gustafsson, T.Hard
Key ref:
H.Baumann et al. (1993). Refined solution structure of the glucocorticoid receptor DNA-binding domain. Biochemistry, 32, 13463-13471. PubMed id: 8257681 DOI: 10.1021/bi00212a011
Date:
15-Mar-94     Release date:   22-Jun-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06536  (GCR_RAT) -  Glucocorticoid receptor from Rattus norvegicus
Seq:
Struc: 		 
Seq:
Struc: 		795 a.a.
72 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi00212a011 Biochemistry 32:13463-13471 (1993)
PubMed id: 8257681  
 
 
Refined solution structure of the glucocorticoid receptor DNA-binding domain.
H.Baumann, K.Paulsen, H.Kovács, H.Berglund, A.P.Wright, J.A.Gustafsson, T.Härd.
 
  ABSTRACT  
 
A refined solution structure of the glucocorticoid receptor DNA-binding domain (GR DBD) has been determined using two- and three-dimensional nuclear magnetic resonance (NMR) spectroscopy on an 15N-labeled GR DBD fragment in conjunction with distance geometry and simulated annealing calculations. Thirty structures of the fragment C440-R510 of the rat GR were calculated based on 906 distance constraints obtained from NOE intensities (168 intraresidue and 738 interresidue NOEs) and 43 dihedral constraints. Average atomic root mean square (rms) differences between the 24 best structures and their geometric average are 0.70 A for backbone atoms and 1.44 A for all heavy atoms. Several regions that were not well defined in a previous NMR structure determination of a similar protein fragment [Härd, T., Kellenbach, E., Boelens, R., Maler, B.A., Dahlman, K., Freedman, L.P., Carlstedt-Duke, J., Yamamoto, K.R., Gustafsson, J.-A., & Kaptein, R. (1990b) Science 249, 157-160] are now well-defined. The refined structure of the uncomplexed GR DBD is very similar to the crystal structure of GR DBD in a sequence specific DNA complex [Luisi, B. F., Xu, W. X., Otwinowski, Z., Freeman, L. P., Yamamoto, K. R., & Sigler, P. B. (1991) Nature 352, 497-505], in particular with regard to the presence and relative positions of secondary structure elements. The backbone atom rms difference between the average NMR solution structure and the crystal structure of the DNA-complexed GR DBD is 1.8 A. The most pronounced differences between the free and DNA-complexed states are found within the fragment C476-C482 in the second zinc-coordinating domain.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
17933688 C.Kremoser, M.Albers, T.P.Burris, U.Deuschle, and M.Koegl (2007).
Panning for SNuRMs: using cofactor profiling for the rational discovery of selective nuclear receptor modulators.
  Drug Discov Today, 12, 860-869.  
17137423 D.L.Bain, A.F.Heneghan, K.D.Connaghan-Jones, and M.T.Miura (2007).
Nuclear receptor structure: implications for function.
  Annu Rev Physiol, 69, 201-220.  
17478511 D.Nguyen, M.Bail, G.Pesant, V.N.Dupont, E.Rouault, J.Deschênes, W.Rocha, G.Melançon, S.V.Steinberg, and S.Mader (2007).
Rational design of an estrogen receptor mutant with altered DNA-binding specificity.
  Nucleic Acids Res, 35, 3465-3477.  
17372357 T.J.Oldfield (2007).
CAALIGN: a program for pairwise and multiple protein-structure alignment.
  Acta Crystallogr D Biol Crystallogr, 63, 514-525.  
14640689 J.C.Payne, B.W.Rous, A.L.Tenderholt, and H.A.Godwin (2003).
Spectroscopic determination of the binding affinity of zinc to the DNA-binding domains of nuclear hormone receptors.
  Biochemistry, 42, 14214-14224.  
12211013 J.Bredenberg, and L.Nilsson (2002).
Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations.
  Proteins, 49, 24-36.  
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.  
10913303 T.Lundbäck, S.van Den Berg, and T.Härd (2000).
Sequence-specific DNA binding by the glucocorticoid receptor DNA-binding domain is linked to a salt-dependent histidine protonation.
  Biochemistry, 39, 8909-8916.  
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.  
10455143 R.Kumar, I.V.Baskakov, G.Srinivasan, D.W.Bolen, J.C.Lee, and E.B.Thompson (1999).
Interdomain signaling in a two-domain fragment of the human glucocorticoid receptor.
  J Biol Chem, 274, 24737-24741.  
  9584182 G.G.Préfontaine, M.E.Lemieux, W.Giffin, C.Schild-Poulter, L.Pope, E.LaCasse, P.Walker, and R.J.Haché (1998).
Recruitment of octamer transcription factors to DNA by glucocorticoid receptor.
  Mol Cell Biol, 18, 3416-3430.  
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.  
8734007 J.H.Pinter, C.Deep, and O.K.Park-Sarge (1996).
Progesterone receptors: expression and regulation in the mammalian ovary.
  Clin Obstet Gynecol, 39, 424-435.  
17029807 T.Härd, and T.Lundbäck (1996).
Thermodynamics of sequence-specific protein-DNA interactions.
  Biophys Chem, 62, 121-139.  
8643475 T.Lundbäck, and T.Härd (1996).
Sequence-specific DNA-binding dominated by dehydration.
  Proc Natl Acad Sci U S A, 93, 4754-4759.  
7664096 D.T.Gewirth, and P.B.Sigler (1995).
The basis for half-site specificity explored through a non-cognate steroid receptor-DNA complex.
  Nat Struct Biol, 2, 386-394.
PDB code: 1lat
7696496 M.A.Eriksson, T.Härd, and L.Nilsson (1995).
Molecular dynamics simulations of the glucocorticoid receptor DNA-binding domain in complex with DNA and free in solution.
  Biophys J, 68, 402-426.  
7925381 M.S.Lee, D.S.Sem, S.A.Kliewer, J.Provencal, R.M.Evans, and P.E.Wright (1994).
NMR assignments and secondary structure of the retinoid X receptor alpha DNA-binding domain. Evidence for the novel C-terminal helix.
  Eur J Biochem, 224, 639-650.  
7765166 S.Campbell-Burk, and S.Zhong (1994).
Biomolecular applications of heteronuclear multidimensional NMR.
  Curr Opin Biotechnol, 5, 346-354.  
16100953 J.W.Schwabe, L.Chapman, J.T.Finch, D.Rhodes, and D.Neuhaus (1993).
DNA recognition by the oestrogen receptor: from solution to the crystal.
  Structure, 1, 187-204.
PDB code: 1hcp
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 code is shown on the right.

 

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