5E6A

Glucocorticoid receptor DNA binding domain - PLAU NF-kB response element complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.197 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Cryptic glucocorticoid receptor-binding sites pervade genomic NF-kappa B response elements.

Hudson, W.H.Vera, I.M.S.Nwachukwu, J.C.Weikum, E.R.Herbst, A.G.Yang, Q.Bain, D.L.Nettles, K.W.Kojetin, D.J.Ortlund, E.A.

(2018) Nat Commun 9: 1337-1337

  • DOI: 10.1038/s41467-018-03780-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the g ...

    Glucocorticoids (GCs) are potent repressors of NF-κB activity, making them a preferred choice for treatment of inflammation-driven conditions. Despite the widespread use of GCs in the clinic, current models are inadequate to explain the role of the glucocorticoid receptor (GR) within this critical signaling pathway. GR binding directly to NF-κB itself-tethering in a DNA binding-independent manner-represents the standing model of how GCs inhibit NF-κB-driven transcription. We demonstrate that direct binding of GR to genomic NF-κB response elements (κBREs) mediates GR-driven repression of inflammatory gene expression. We report five crystal structures and solution NMR data of GR DBD-κBRE complexes, which reveal that GR recognizes a cryptic response element between the binding footprints of NF-κB subunits within κBREs. These cryptic sequences exhibit high sequence and functional conservation, suggesting that GR binding to κBREs is an evolutionarily conserved mechanism of controlling the inflammatory response.


    Organizational Affiliation

    Department of Molecular Therapeutics, The Scripps Research Institute, Jupiter, Florida, 33458, USA.,Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, 80045​, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA. eortlun@emory.edu.,Department of Pharmacology and Physiology, Saint Louis University School of Medicine, Saint Louis, MO, 63104, USA.,Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, 30322, USA.,Discovery and Developmental Therapeutics, Winship Cancer Institute, Atlanta, Georgia, 30322, USA.,Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, 30322, USA.,Department of Integrated Structural and Computational Biology, The Scripps Research Institute, Jupiter, Florida, 33458, USA.,Discovery and Developmental Therapeutics, Winship Cancer Institute, Atlanta, Georgia, 30322, USA. eortlun@emory.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B
114Homo sapiensMutation(s): 0 
Gene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*TP*GP*AP*T)-3')C16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*AP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*AP*G)-3')D16Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.197 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.993α = 90.00
b = 95.497β = 90.00
c = 103.634γ = 90.00
Software Package:
Software NamePurpose
SERGUIdata collection
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-02-08
    Type: Initial release
  • Version 1.1: 2018-10-24
    Type: Data collection, Database references