3G9J

GR DNA binding domain:Pal, 18bp complex-36

• PDB DOI:  https://doi.org/10.2210/pdb3G9J/pdb
• NAKB: 3G9J

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


• Deposited: 2009-02-13 Released: 2009-04-21 
• Deposition Author(s): Pufall, M.A., Yamamoto, K.R., Meijsing, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.188 

Literature

DNA binding site sequence directs glucocorticoid receptor structure and activity.

Meijsing, S.H., Pufall, M.A., So, A.Y., Bates, D.L., Chen, L., Yamamoto, K.R.

(2009) Science 324: 407-410

• PubMed: 19372434 
• DOI: https://doi.org/10.1126/science.1164265
• Primary Citation of Related Structures:  
  3FYL, 3G6P, 3G6Q, 3G6R, 3G6T, 3G6U, 3G8U, 3G8X, 3G97, 3G99, 3G9I, 3G9J, 3G9M, 3G9O, 3G9P


• PubMed Abstract: 
  

Genes are not simply turned on or off, but instead their expression is fine-tuned to meet the needs of a cell. How genes are modulated so precisely is not well understood. The glucocorticoid receptor (GR) regulates target genes by associating with specific DNA binding sites, the sequences of which differ between genes. Traditionally, these binding sites have been viewed only as docking sites. Using structural, biochemical, and cell-based assays, we show that GR binding sequences, differing by as little as a single base pair, differentially affect GR conformation and regulatory activity. We therefore propose that DNA is a sequence-specific allosteric ligand of GR that tailors the activity of the receptor toward specific target genes.

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Organizational Affiliation: 

Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 31.43 kDa 
• Atom Count: 2,052 
• Modelled Residue Count: 189 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	C [auth A], D [auth B]	90	Rattus norvegicus	Mutation(s): 0  Gene Names: Nr3c1, Grl
UniProt
Find proteins for P06536 (Rattus norvegicus) Explore P06536  Go to UniProtKB:  P06536

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*TP*G)-3')	A [auth C]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*TP*G)-3')	B [auth D]	18	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	F [auth A], G [auth A], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	E [auth C], H [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.32 Å
• R-Value Free: 0.226 
• R-Value Work: 0.184 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.069	α = 90
b = 102.096	β = 90
c = 112.076	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Pufall, M.A., Yamamoto, K.R., Meijsing, S.H.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description