5VA0

Glucocorticoid Receptor DNA Binding Domain in complex with AP-1 response element from VCAM-1 Promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.295 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Tethering not required: the glucocorticoid receptor binds directly to activator protein-1 recognition motifs to repress inflammatory genes.

Weikum, E.R.de Vera, I.M.S.Nwachukwu, J.C.Hudson, W.H.Nettles, K.W.Kojetin, D.J.Ortlund, E.A.

(2017) Nucleic Acids Res. 45: 8596-8608

  • DOI: 10.1093/nar/gkx509
  • Primary Citation of Related Structures:  5VA7

  • PubMed Abstract: 
  • The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achie ...

    The glucocorticoid receptor (GR) is a ligand-regulated transcription factor that controls the expression of extensive gene networks, driving both up- and down-regulation. GR utilizes multiple DNA-binding-dependent and -independent mechanisms to achieve context-specific transcriptional outcomes. The DNA-binding-independent mechanism involves tethering of GR to the pro-inflammatory transcription factor activator protein-1 (AP-1) through protein-protein interactions. This mechanism has served as the predominant model of GR-mediated transrepression of inflammatory genes. However, ChIP-seq data have consistently shown GR to occupy AP-1 response elements (TREs), even in the absence of AP-1. Therefore, the current model is insufficient to explain GR action at these sites. Here, we show that GR regulates a subset of inflammatory genes in a DNA-binding-dependent manner. Using structural biology and biochemical approaches, we show that GR binds directly to TREs via sequence-specific contacts to a GR-binding sequence (GBS) half-site found embedded within the TRE motif. Furthermore, we show that GR-mediated transrepression observed at TRE sites to be DNA-binding-dependent. This represents a paradigm shift in the field, showing that GR uses multiple mechanisms to suppress inflammatory gene expression. This work further expands our understanding of this complex multifaceted transcription factor.


    Organizational Affiliation

    Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B
72Homo sapiensGene 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*GP*GP*CP*TP*GP*AP*CP*TP*CP*AP*TP*CP*AP*AP*G)-3')C16Homo sapiens
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*TP*GP*AP*TP*GP*AP*GP*TP*CP*AP*GP*CP*CP*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: 2.295 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.197 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.442α = 90.00
b = 96.280β = 90.00
c = 105.223γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-16
    Type: Database references, Refinement description
  • Version 1.2: 2017-09-13
    Type: Database references