4A2J

PR X-Ray structures in agonist conformations reveal two different mechanisms for partial agonism in 11beta-substituted steroids


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structures of progesterone receptor ligand binding domain in its agonist state reveal differing mechanisms for mixed profiles of 11 beta-substituted steroids.

Lusher, S.J.Raaijmakers, H.C.Vu-Pham, D.Kazemier, B.Bosch, R.McGuire, R.Azevedo, R.Hamersma, H.Dechering, K.Oubrie, A.van Duin, M.de Vlieg, J.

(2012) J. Biol. Chem. 287: 20333-20343

  • DOI: 10.1074/jbc.M111.308403
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We present here the x-ray structures of the progesterone receptor (PR) in complex with two mixed profile PR modulators whose functional activity results from two differing molecular mechanisms. The structure of Asoprisnil bound to the agonist state o ...

    We present here the x-ray structures of the progesterone receptor (PR) in complex with two mixed profile PR modulators whose functional activity results from two differing molecular mechanisms. The structure of Asoprisnil bound to the agonist state of PR demonstrates the contribution of the ligand to increasing stability of the agonist conformation of helix-12 via a specific hydrogen-bond network including Glu(723). This interaction is absent when the full antagonist, RU486, binds to PR. Combined with a previously reported structure of Asoprisnil bound to the antagonist state of the receptor, this structure extends our understanding of the complex molecular interactions underlying the mixed agonist/antagonist profile of the compound. In addition, we present the structure of PR in its agonist conformation bound to the mixed profile compound Org3H whose reduced antagonistic activity and increased agonistic activity compared with reference antagonists is due to an induced fit around Trp(755), resulting in a decreased steric clash with Met(909) but inducing a new internal clash with Val(912) in helix-12. This structure also explains the previously published observation that 16α attachments to RU486 analogs induce mixed profiles by altering the binding of 11β substituents. Together these structures further our understanding of the steric and electrostatic factors that contribute to the function of steroid receptor modulators, providing valuable insight for future compound design.


    Organizational Affiliation

    Departments of Molecular Design and Informatics, MSD, P. O. Box 20, 5340 BH, Oss, The Netherlands.s.lusher@esciencecenter.nl




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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
AS0
Query on AS0

Download SDF File 
Download CCD File 
A, B
4-[(11BETA,17BETA)-17-METHOXY-17-(METHOXYMETHYL)-3-OXOESTRA-4,9-DIEN-11-YL]BENZALDEHYDE OXIME
C28 H35 N O4
GJMNAFGEUJBOCE-MEQIQULJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.614α = 90.00
b = 64.696β = 95.71
c = 69.991γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOSFLMdata reduction
REFMACphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-04
    Type: Initial release
  • Version 1.1: 2012-07-04
    Type: Other
  • Version 1.2: 2018-02-07
    Type: Database references, Experimental preparation