1HJ1

RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PURE ANTIOESTROGEN ICI164,384


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Structural Insights Into the Mode of Action of a Pure Antiestrogen

Pike, A.C.W.Brzozowski, A.M.Walton, J.Hubbard, R.E.Thorsell, A.G.Li, Y.L.Gustafsson, J.A.Carlquist, M.

(2001) Structure 9: 145

  • DOI: https://doi.org/10.1016/s0969-2126(01)00568-8
  • Primary Citation of Related Structures:  
    1HJ1

  • PubMed Abstract: 

    Estrogens exert their effects on target tissues by binding to a nuclear transcription factor termed the estrogen receptor (ER). Previous structural studies have demonstrated that each class of ER ligand (agonist, partial agonist, and SERM antagonist) induces distinctive orientations in the receptor's carboxy-terminal transactivation helix. The conformation of this portion of the receptor determines whether ER can recruit and interact with the components of the transcriptional machinery, thereby facilitating target gene expression. We have determined the structure of rat ERbeta ligand binding domain (LBD) in complex with the pure antiestrogen ICI 164,384 at 2.3 A resolution. The binding of this compound to the receptor completely abolishes the association between the transactivation helix (H12) and the rest of the LBD. The structure reveals that the terminal portion of ICI's bulky side chain substituent protrudes from the hormone binding pocket, binds along the coactivator recruitment site, and physically prevents H12 from adopting either its characteristic agonist or AF2 antagonist orientation. The binding mode adopted by the pure antiestrogen is similar to that seen for other ER antagonists. However, the size and resultant positioning of the ligand's side chain substituent produces a receptor conformation that is distinct from that adopted in the presence of other classes of ER ligands. The novel observation that binding of ICI results in the complete destabilization of H12 provides some indications as to a possible mechanism for pure receptor antagonism.


  • Organizational Affiliation

    Structural Biology Laboratory, Chemistry Department, University of York, Heslington, YO10 5DD, York, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OESTROGEN RECEPTOR BETA255Rattus norvegicusMutation(s): 0 
Gene Names: OESTROGEN RECEPTOR BETA
UniProt
Find proteins for Q62986 (Rattus norvegicus)
Explore Q62986 
Go to UniProtKB:  Q62986
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62986
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AOE
Query on AOE

Download Ideal Coordinates CCD File 
B [auth A]N-BUTYL-11-[(7R,8R,9S,13S,14S,17S)-3,17-DIHYDROXY-13-METHYL-7,8,9,11,12,13,14,15,16,17-DECAHYDRO-6H-CYCLOPENTA[A]PHENANTHREN-7-YL]-N-METHYLUNDECANAMIDE
C34 H55 N O3
BVVFOLSZMQVDKV-KXQIQQEYSA-N
PMB
Query on PMB

Download Ideal Coordinates CCD File 
C [auth A]PARA-MERCURY-BENZENESULFONIC ACID
C6 H5 Hg O3 S
KQAOIKIZSJJTII-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
AOE BindingDB:  1HJ1 Ki: min: 1.5, max: 4.6 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.220 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.38α = 90
b = 82.67β = 90
c = 106.34γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4phasing
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-04
    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: 2018-10-24
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description