3G99

GR DNA binding domain:Pal complex-9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 10.1126/science.1164265
  • Primary Citation of Related Structures:  
    3G6R, 3G6T, 3G6U, 3G6P, 3G6Q, 3G8U, 3G97, 3G8X, 3G99, 3G9M

  • 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 sp ...

    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.


    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptorAB90Rattus norvegicusMutation(s): 0 
Gene Names: GrlNr3c1
Find proteins for P06536 (Rattus norvegicus)
Explore P06536 
Go to UniProtKB:  P06536
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)-3')D16N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*TP*CP*T)-3')C16N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      BR
      Query on BR

      Download CCD File 
      C
      BROMIDE ION
      Br
      CPELXLSAUQHCOX-UHFFFAOYSA-M
       Ligand Interaction
      ZN
      Query on ZN

      Download CCD File 
      A, B
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      EDO
      Query on EDO

      Download CCD File 
      A, D
      1,2-ETHANEDIOL
      C2 H6 O2
      LYCAIKOWRPUZTN-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.81 Å
      • R-Value Free: 0.230 
      • R-Value Work: 0.191 
      • R-Value Observed: 0.194 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 116.774α = 90
      b = 38.189β = 123.11
      c = 97.064γ = 90
      Software Package:
      Software NamePurpose
      Blu-Icedata collection
      PHENIXmodel building
      PHENIXrefinement
      HKL-2000data reduction
      HKL-2000data scaling
      PHENIXphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      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