1QKM

HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 BETAA255Homo sapiensMutation(s): 0 
Gene Names: OESTROGEN RECEPTOR BETA, ESR2, ESTRB, NR3A2
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
NIH Common Fund Data Resources
PHAROS  Q92731
GTEx  ENSG00000140009
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEN
Query on GEN
Download CCD File 
A
GENISTEIN
C15 H10 O5
TZBJGXHYKVUXJN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GENIC50:  1.2999999523162842   nM  BindingDB
GENIC50:  6.800000190734863   nM  BindingDB
GENIC50:  200   nM  BindingDB
GENEC50:  200   nM  BindingDB
GENIC50:  98.69999694824219   nM  BindingDB
GENKi:  24   nM  BindingDB
GENIC50:  18   nM  BindingDB
GENIC50:  61   nM  BindingDB
GENIC50:  4   nM  BindingDB
GENIC50:  25   nM  BindingDB
GENIC50:  390   nM  BindingDB
GENIC50:  395   nM  BindingDB
GENEC50:  6   nM  BindingDB
GENIC50:  83   nM  BindingDB
GENIC50:  9.699999809265137   nM  BindingDB
GENEC50:  28   nM  BindingDB
GENIC50:  10   nM  BindingDB
GENEC50:  73   nM  BindingDB
GENEC50:  4.099999904632568   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.215 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.12α = 90
b = 63.12β = 90
c = 250.23γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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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