3H52

Crystal structure of the antagonist form of human glucocorticoid receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 

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
  • Primary Citation of Related Structures:  
    3H52

  • 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 the nuclear receptor corepressor (NCoR) ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glucocorticoid receptor ABCD254Homo sapiensMutation(s): 5 
Gene Names: NR3C1GRL
Find proteins for P04150 (Homo sapiens)
Explore P04150 
Go to UniProtKB:  P04150
NIH Common Fund Data Resources
PHAROS:  P04150
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor corepressor 1 MN19N/AMutation(s): 0 
Find proteins for O75376 (Homo sapiens)
Explore O75376 
Go to UniProtKB:  O75376
NIH Common Fund Data Resources
PHAROS:  O75376
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
486
Query on 486

Download Ideal Coordinates 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
C29 H35 N O2
VKHAHZOOUSRJNA-GCNJZUOMSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
486Ki:  1.2000000476837158   nM  BindingDB
486IC50:  18   nM  BindingDB
486EC50:  2.5   nM  BindingDB
486IC50:  8.699999809265137   nM  BindingDB
486IC50:  0.6000000238418579   nM  BindingDB
486IC50:  15   nM  BindingDB
486IC50:  13   nM  BindingDB
486Ki:  0.4000000059604645   nM  BindingDB
486IC50:  3.299999952316284   nM  BindingDB
486IC50:  6.309999942779541   nM  BindingDB
486EC50:  4.800000190734863   nM  BindingDB
486IC50:  0.30000001192092896   nM  BindingDB
486IC50:  5.75   nM  BindingDB
486IC50:  6   nM  BindingDB
486Ki:  120   nM  BindingDB
486IC50:  0.800000011920929   nM  BindingDB
486IC50:  5   nM  BindingDB
486Ki:  0.6800000071525574   nM  BindingDB
486IC50:  1.100000023841858   nM  BindingDB
486EC50:  2   nM  BindingDB
486Ki:  0.4399999976158142   nM  BindingDB
486Ki:  0.10000000149011612   nM  BindingDB
486IC50:  11   nM  BindingDB
486IC50:  1.600000023841858   nM  BindingDB
486Ki:  169   nM  BindingDB
486Ki:  0.23999999463558197   nM  BindingDB
486IC50:  3.200000047683716   nM  BindingDB
486Ki:  0.8199999928474426   nM  BindingDB
486IC50:  1   nM  BindingDB
486EC50:  2500   nM  BindingDB
486Ki:  0.09000000357627869   nM  BindingDB
486Ki:  1   nM  BindingDB
486IC50:  2.200000047683716   nM  BindingDB
486IC50:  1.899999976158142   nM  BindingDB
486IC50:  5.800000190734863   nM  BindingDB
486Ki:  0.10000000149011612   nM  BindingDB
486Ki:  3   nM  BindingDB
486IC50:  4.800000190734863   nM  BindingDB
486IC50:  6.900000095367432   nM  BindingDB
486EC50:  872   nM  BindingDB
486IC50:  1.399999976158142   nM  BindingDB
486Ki:  0.30000001192092896   nM  BindingDB
486EC50:  0.6000000238418579   nM  BindingDB
486Ki:  6   nM  BindingDB
486Ki:  1.100000023841858   nM  BindingDB
486Ki:  5   nM  BindingDB
486Ki:  0.8399999737739563   nM  BindingDB
486IC50:  4.699999809265137   nM  BindingDB
486IC50:  4.679999828338623   nM  BindingDB
486IC50:  0.009999999776482582   nM  BindingDB
486IC50:  0.949999988079071   nM  BindingDB
486IC50:  33   nM  BindingDB
486IC50:  20   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.228 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.53α = 90
b = 99.53β = 90
c = 252.43γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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