1QKN

RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH ANTAGONIST RALOXIFENE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist

Pike, A.C.W.Brzozowski, A.M.Hubbard, R.E.Bonn, T.Thorsell, A.-G.Engstrom, O.Ljunggren, J.Gustaffson, J.-A.Carlquist, M.

(1999) EMBO J 18: 4608

  • DOI: 10.1093/emboj/18.17.4608
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Oestrogens exert their physiological effects through two receptor subtypes. Here we report the three-dimensional structure of the oestrogen receptor beta isoform (ERbeta) ligand-binding domain (LBD) in the presence of the phyto-oestrogen genistein an ...

    Oestrogens exert their physiological effects through two receptor subtypes. Here we report the three-dimensional structure of the oestrogen receptor beta isoform (ERbeta) ligand-binding domain (LBD) in the presence of the phyto-oestrogen genistein and the antagonist raloxifene. The overall structure of ERbeta-LBD is very similar to that previously reported for ERalpha. Each ligand interacts with a unique set of residues within the hormone-binding cavity and induces a distinct orientation in the AF-2 helix (H12). The bulky side chain of raloxifene protrudes from the cavity and physically prevents the alignment of H12 over the bound ligand. In contrast, genistein is completely buried within the hydrophobic core of the protein and binds in a manner similar to that observed for ER's endogenous hormone, 17beta-oestradiol. However, in the ERbeta-genistein complex, H12 does not adopt the distinctive 'agonist' position but, instead, lies in a similar orientation to that induced by ER antagonists. Such a sub-optimal alignment of the transactivation helix is consistent with genistein's partial agonist character in ERbeta and demonstrates how ER's transcriptional response to certain bound ligands is attenuated.


    Related Citations: 
    • Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor
      Brzozowski, A.M., Pike, A.C.W., Dauter, Z., Hubbard, R.E., Bonn, T., Engstrom, O., Ohman, L., Greene, G.L., Gustaffson, J.-A., Carlquist, M.
      (1997) Nature 389: 753

    Organizational Affiliation

    Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ESTROGEN RECEPTOR BETAA255Rattus norvegicusMutation(s): 0 
Gene Names: OESTROGEN RECEPTOR BETAEsr2ErbetaNr3a2
Find proteins for Q62986 (Rattus norvegicus)
Explore Q62986 
Go to UniProtKB:  Q62986
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAL
Query on RAL

Download CCD File 
A
RALOXIFENE
C28 H27 N O4 S
GZUITABIAKMVPG-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RALKi:  4.5   nM  BindingDB
RALIC50:  4   nM  BindingDB
RALIC50:  6.900000095367432   nM  BindingDB
RALIC50:  3.4000000953674316   nM  BindingDB
RALIC50:  18.899999618530273   nM  BindingDB
RALIC50 :  3.4000000953674316   nM  PDBBind
RALKi:  10   nM  BindingDB
RALIC50:  1.899999976158142   nM  BindingDB
RALEC50:  341   nM  BindingDB
RALIC50:  7.699999809265137   nM  BindingDB
RALIC50:  170   nM  BindingDB
RALIC50:  0.3400000035762787   nM  BindingDB
RALIC50:  12   nM  BindingDB
RALEC50:  4.320000171661377   nM  BindingDB
RALIC50:  15   nM  BindingDB
RALKi:  23   nM  BindingDB
RALIC50:  0.20000000298023224   nM  BindingDB
RALIC50:  260   nM  BindingDB
RALIC50:  470   nM  BindingDB
RALIC50:  8.199999809265137   nM  BindingDB
RALKi:  2.740000009536743   nM  BindingDB
RALIC50:  470   nM  BindingDB
RALKi:  4.300000190734863   nM  BindingDB
RALIC50:  1.600000023841858   nM  BindingDB
RALIC50:  557   nM  BindingDB
RALIC50:  43   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • Space Group: P 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.55α = 90
b = 67.55β = 90
c = 148.2γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection