5DXM

Crystal Structure of the ER-alpha Ligand-binding Domain in Complex with the Cyclofenil Derivative 3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Predictive features of ligand-specific signaling through the estrogen receptor.

Nwachukwu, J.C., Srinivasan, S., Zheng, Y., Wang, S., Min, J., Dong, C., Liao, Z., Nowak, J., Wright, N.J., Houtman, R., Carlson, K.E., Josan, J.S., Elemento, O., Katzenellenbogen, J.A., Zhou, H.B., Nettles, K.W.

(2016) Mol.Syst.Biol. 12: 864-864

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Some estrogen receptor-α (ERα)-targeted breast cancer therapies such as tamoxifen have tissue-selective or cell-specific activities, while others have similar activities in different cell types. To identify biophysical determinants of cell-specific s ...

    Some estrogen receptor-α (ERα)-targeted breast cancer therapies such as tamoxifen have tissue-selective or cell-specific activities, while others have similar activities in different cell types. To identify biophysical determinants of cell-specific signaling and breast cancer cell proliferation, we synthesized 241 ERα ligands based on 19 chemical scaffolds, and compared ligand response using quantitative bioassays for canonical ERα activities and X-ray crystallography. Ligands that regulate the dynamics and stability of the coactivator-binding site in the C-terminal ligand-binding domain, called activation function-2 (AF-2), showed similar activity profiles in different cell types. Such ligands induced breast cancer cell proliferation in a manner that was predicted by the canonical recruitment of the coactivators NCOA1/2/3 and induction of the GREB1 proliferative gene. For some ligand series, a single inter-atomic distance in the ligand-binding domain predicted their proliferative effects. In contrast, the N-terminal coactivator-binding site, activation function-1 (AF-1), determined cell-specific signaling induced by ligands that used alternate mechanisms to control cell proliferation. Thus, incorporating systems structural analyses with quantitative chemical biology reveals how ligands can achieve distinct allosteric signaling outcomes through ERα.

    Organizational Affiliation: 

    Department of Cancer Biology, The Scripps Research Institute, Jupiter, FL, 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
14Homo 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
5J0
Query on 5J0
Download SDF File 
Download CCD File 
A, B
3-[(E)-(1s,5s)-bicyclo[3.3.1]non-9-ylidene(4-hydroxyphenyl)methyl]phenol
C22 H24 O2
MPHSLLGYXNIWMO-MVFCNCFGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.506α = 90.00
b = 82.034β = 111.06
c = 58.843γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release