1R4O | pdb_00001r4o

Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA

• PDB DOI: https://doi.org/10.2210/pdb1R4O/pdb
• NAKB: 1R4O

• Classification: TRANSCRIPTION/DNA
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-10-07 Released: 2003-10-21 
• Deposition Author(s): Luisi, B.F., Xu, W.X., Otwinowski, Z., Freedman, L.P., Yamamoto, K.R., Sigler, P.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 
  0.271 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

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: 497-505

• PubMed: 1865905 
• DOI: https://doi.org/10.1038/352497a0
• Primary Citation Related Structures: 
  1GLU, 1R4O, 1R4R


• PubMed Abstract: 
  

  Two crystal structures of the glucocorticoid receptor DNA-binding domain complexed with DNA are reported. The domain has a globular fold which contains two Zn-nucleated substructures of distinct conformation and function. When it binds DNA, the domain dimerizes, placing the subunits in adjacent major grooves. In one complex, the DNA has the symmetrical consensus target sequence; in the second, the central spacing between the target's half-sites is larger by one base pair. This results in one subunit interacting specifically with the consensus target half-site and the other nonspecifically with a noncognate element. The DNA-induced dimer fixes the separation of the subunits' recognition surfaces so that the spacing between the half-sites becomes a critical feature of the target sequence's identity.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.34 kDa 
• Atom Count: 2,121 
• Modeled Residue Count: 198 
• Deposited Residue Count: 222 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	C [auth A], D [auth B]	92	Rattus norvegicus	Mutation(s): 0  Gene Names: NR3C1 OR GRL
UniProt
Find proteins for P06536 (Rattus norvegicus) Explore P06536  Go to UniProtKB:  P06536

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*CP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3'	A [auth C], B [auth D]	19	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work:  0.271 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.5	α = 90
b = 97.5	β = 90
c = 120.5	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-10-21 
Deposition Author(s): Luisi, B.F., Xu, W.X., Otwinowski, Z., Freedman, L.P., Yamamoto, K.R., Sigler, P.B.

Revision History  

• Version 1.0: 2003-10-21
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2014-01-22
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description