Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.09 kDa 
• Atom Count: 550 
• Modelled Residue Count: 71 
• Deposited Residue Count: 71 
• Unique protein chains: 1

1RGD

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

• PDB DOI: 10.2210/pdb1RGD/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Mutation(s): No 


• Deposited: 1995-01-06 Released: 1995-02-14 
• Deposition Author(s): Van Tilborg, M.A.A., Bonvin, A.M.J.J., Hard, K., Davis, A., Maler, B., Boelens, R., Yamamoto, K.R., Kaptein, R.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Submitted: 11 

Literature

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

van Tilborg, M.A., Bonvin, A.M., Hard, K., Davis, A.L., Maler, B., Boelens, R., Yamamoto, K.R., Kaptein, R.

(1995) J Mol Biol 247: 689-700

• PubMed: 7723024 
• DOI: 10.1006/jmbi.1995.0173
• Primary Citation of Related Structures:  
  1RGD


• PubMed 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.

---

Related Citations: 

• Crystallographic Analysis of the Interaction of the Glucocorticoid Receptor with DNA
  Luisi, B.F., Xu, W.X., Otwinowski, Z., Freedman, L.P., Yamamoto, K.R., Sigler, P.B.
  (1991) Nature 352: 497

• Solution Structure of the Glucocorticoid Receptor DNA-Binding Domain
  Hard, T., Kellenbach, E., Boelens, R., Maler, B.A., Dahlman, K., Freedman, L.P., Carlstedt-Duke, J., Yamamoto, K.R., Gustafsson, J.-A., Kaptein, R.
  (1990) Science 249: 157

• 1H NMR Studies of the Glucocorticoid Receptor DNA-Binding Domain: Sequential Assignments and Identification of Secondary Structure Elements
  Hard, T., Kellenbach, E., Boelens, R., Kaptein, R., Dahlman, K., Carlstedt-Duke, J., Freedman, L.P., Maler, B.A., Hyde, E., Gustafsson, J.-A., Yamamoto, K.R.
  (1990) Biochemistry 29: 9015

---

Organizational Affiliation: 

Bijvoet Center for Biomolecular Research Utrecht University, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUCOCORTICOID RECEPTOR	A	71	Rattus norvegicus	Mutation(s): 0  Gene Names: Nr3c1, Grl
UniProt
Find proteins for P06536 (Rattus norvegicus) Explore P06536  Go to UniProtKB:  P06536

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Submitted: 11 
• OLDERADO: 1RGD Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-01-06 
• Released Date: 1995-02-14 
Deposition Author(s): Van Tilborg, M.A.A., Bonvin, A.M.J.J., Hard, K., Davis, A., Maler, B., Boelens, R., Yamamoto, K.R., Kaptein, R.

Revision History  

• Version 1.0: 1995-02-14
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations, Other, Structure summary