2W8Y

RU486 bound to the progesterone receptor in a destabilized agonistic conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The X-Ray Structure of Ru486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation.

Raaijmakers, H.C.A.Versteegh, J.Uitdehaag, J.C.M.

(2009) J.Biol.Chem. 284: 19572

  • DOI: 10.1074/jbc.M109.007872

  • PubMed Abstract: 
  • Here we describe the 1.95 A structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist nore ...

    Here we describe the 1.95 A structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist norethindrone and soaking it in a solution containing the antagonist RU486 for extended times. Clear ligand exchange could be observed in one copy of the PR ligand binding domain dimer in the crystal. RU486 binds while PR is in an agonistic conformation without displacing helix 12. Although this is probably because of the constraints of the crystal lattice, it demonstrates that helix 12 displacement is not a prerequisite for RU486 binding. Interestingly, B-factor analysis clearly shows that helix 12 becomes more flexible after RU486 binding, suggesting that RU486, being a model antagonist, does not induce one fixed conformation of helix 12 but changes its positional equilibrium. This conclusion is confirmed by comparing the structures of RU486 bound to PR and RU486 bound to the glucocorticoid receptor.


    Organizational Affiliation

    Departments of Molecular Design and Informatics, Molecular Pharmacology and DMPK, Schering-Plough Research Institute, P. O. Box 20, 5340 BH Oss, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROGESTERONE RECEPTOR
A, B
260Homo sapiensMutation(s): 0 
Gene Names: PGR (NR3C3)
Find proteins for P06401 (Homo sapiens)
Go to Gene View: PGR
Go to UniProtKB:  P06401
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
486
Query on 486

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Download CCD File 
A
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
EDO
Query on EDO

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Download CCD File 
B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NDR
Query on NDR

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Download CCD File 
B
(14beta,17alpha)-17-ethynyl-17-hydroxyestr-4-en-3-one
C20 H26 O2
VIKNJXKGJWUCNN-XGXHKTLJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.164α = 90.00
b = 63.897β = 95.57
c = 70.051γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2017-12-27
    Type: Advisory, Structure summary