3H52

Crystal structure of the antagonist form of human glucocorticoid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular switch in the glucocorticoid receptor: active and passive antagonist conformations

Schoch, G.A.D'Arcy, B.Stihle, M.Burger, D.Bar, D.Benz, J.Thoma, R.Ruf, A.

(2010) J.Mol.Biol. 395: 568-577

  • DOI: 10.1016/j.jmb.2009.11.011

  • PubMed Abstract: 
  • Mifepristone is known to induce mixed passive antagonist, active antagonist, and agonist effects via the glucocorticoid receptor (GR) pathway. Part of the antagonist effects of mifepristone are due to the repression of gene transcription mediated by ...

    Mifepristone is known to induce mixed passive antagonist, active antagonist, and agonist effects via the glucocorticoid receptor (GR) pathway. Part of the antagonist effects of mifepristone are due to the repression of gene transcription mediated by the nuclear receptor corepressor (NCoR). Here, we report the crystal structure of a ternary complex of the GR ligand binding domain (GR-LBD) with mifepristone and a receptor-interacting motif of NCoR. The structures of three different conformations of the GR-LBD mifepristone complex show in the oxosteroid hormone receptor family how helix 12 modulates LBD corepressor and coactivator binding. Differences in NCoR binding and in helix 12 conformation reveal how the 11beta substituent in mifepristone triggers the helix 12 molecular switch to reshape the coactivator site into the corepressor site. Two observed conformations exemplify the active antagonist state of GR with NCoR bound. In another conformation, helix 12 completely blocks the coregulator binding site and explains the passive antagonistic effect of mifepristone on GR.


    Organizational Affiliation

    F Hoffmann-La Roche Ltd, Pharma Research, Discovery Technologies, Grenzacherstrasse 124, CH-4070 Basel, Switzerland. guillaume.schoch@roche.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glucocorticoid receptor
A, B, C, D
254Homo sapiensGene Names: NR3C1 (GRL)
Find proteins for P04150 (Homo sapiens)
Go to Gene View: NR3C1
Go to UniProtKB:  P04150
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor corepressor 1
N, M
19Homo sapiensGene Names: NCOR1 (KIAA1047)
Find proteins for O75376 (Homo sapiens)
Go to Gene View: NCOR1
Go to UniProtKB:  O75376
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
486
Query on 486

Download SDF File 
Download CCD File 
A, B, C, D
11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE
RU-486, MIFEPRISTONE
C29 H35 N O2
VKHAHZOOUSRJNA-GCNJZUOMSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
486IC50: 0 - 11 nM (98) BINDINGDB
486EC50: 0.6 - 872 nM (98) BINDINGDB
486Ki: 0.1 - 169 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.530α = 90.00
b = 99.530β = 90.00
c = 252.430γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2014-02-05
    Type: Database references, Refinement description