5TMT

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with 4,4'-((1,3-dihydro-2H-inden-2-ylidene)methylene)diphenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.051 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Systems Structural Biology Analysis of Ligand Effects on ER alpha Predicts Cellular Response to Environmental Estrogens and Anti-hormone Therapies.

Nwachukwu, J.C.Srinivasan, S.Bruno, N.E.Nowak, J.Wright, N.J.Minutolo, F.Rangarajan, E.S.Izard, T.Yao, X.Q.Grant, B.J.Kojetin, D.J.Elemento, O.Katzenellenbogen, J.A.Nettles, K.W.

(2017) Cell Chem Biol 24: 35-45

  • DOI: 10.1016/j.chembiol.2016.11.014
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Environmental estrogens and anti-hormone therapies for breast cancer have diverse tissue- and signaling-pathway-selective outcomes, but how estrogen receptor alpha (ERα) mediates this phenotypic diversity is poorly understood. We implemented a statis ...

    Environmental estrogens and anti-hormone therapies for breast cancer have diverse tissue- and signaling-pathway-selective outcomes, but how estrogen receptor alpha (ERα) mediates this phenotypic diversity is poorly understood. We implemented a statistical approach to allow unbiased, parallel analyses of multiple crystal structures, and identified subtle perturbations of ERα structure by different synthetic and environmental estrogens. Many of these perturbations were in the sub-Å range, within the noise of the individual structures, but contributed significantly to the activities of synthetic and environmental estrogens. Combining structural perturbation data from many structures with quantitative cellular activity profiles of the ligands enabled identification of structural rules for ligand-specific allosteric signaling-predicting activity from structure. This approach provides a framework for understanding the diverse effects of environmental estrogens and for guiding iterative medicinal chemistry efforts to generate improved breast cancer therapies, an approach that can be applied to understanding other ligand-regulated allosteric signaling pathways.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA. Electronic address: knettles@scripps.edu.,Dipartimento di Farmacia, Università di Pisa, Via Bonanno 33, 56126 Pisa, Italy.,Department of Chemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA.,Department of Molecular Therapeutics, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medical College, 1305 York Avenue, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B
257Homo sapiensMutation(s): 1 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 2
C, D
13Homo sapiensMutation(s): 0 
Gene Names: NCOA2 (BHLHE75, SRC2, TIF2)
Find proteins for Q15596 (Homo sapiens)
Go to Gene View: NCOA2
Go to UniProtKB:  Q15596
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7FJ
Query on 7FJ

Download SDF File 
Download CCD File 
A, B
4,4'-[(1,3-dihydro-2H-inden-2-ylidene)methylene]diphenol
C22 H18 O2
GYIQBNATKDEJGJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.051 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.878α = 90.00
b = 82.220β = 110.14
c = 58.576γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description