2QGW

Crystal Structure of the Estrogen Receptor Alpha Ligand Binding Domain Complexed with a Chloro-Indazole Compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

NFkappaB selectivity of estrogen receptor ligands revealed by comparative crystallographic analyses

Nettles, K.W.Bruning, J.B.Gil, G.Nowak, J.Sharma, S.K.Hahm, J.B.Kulp, K.Hochberg, R.B.Zhou, H.Katzenellenbogen, J.A.Katzenellenbogen, B.S.Kim, Y.Joachmiak, A.Greene, G.L.

(2008) Nat.Chem.Biol. 4: 241-247

  • DOI: 10.1038/nchembio.76
  • Primary Citation of Related Structures:  2B23, 2QA6, 2QA8, 2QAB, 2QGT, 2QH6, 2QR9, 2QSE, 2QXM

  • PubMed Abstract: 
  • Our understanding of how steroid hormones regulate physiological functions has been significantly advanced by structural biology approaches. However, progress has been hampered by misfolding of the ligand binding domains in heterologous expression sy ...

    Our understanding of how steroid hormones regulate physiological functions has been significantly advanced by structural biology approaches. However, progress has been hampered by misfolding of the ligand binding domains in heterologous expression systems and by conformational flexibility that interferes with crystallization. Here, we show that protein folding problems that are common to steroid hormone receptors are circumvented by mutations that stabilize well-characterized conformations of the receptor. We use this approach to present the structure of an apo steroid receptor that reveals a ligand-accessible channel allowing soaking of preformed crystals. Furthermore, crystallization of different pharmacological classes of compounds allowed us to define the structural basis of NFkappaB-selective signaling through the estrogen receptor, thus revealing a unique conformation of the receptor that allows selective suppression of inflammatory gene expression. The ability to crystallize many receptor-ligand complexes with distinct pharmacophores allows one to define structural features of signaling specificity that would not be apparent in a single structure.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, 5353 Parkside Drive, Jupiter, Florida 33458, USA. knettles@scripps.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
A, B
258Homo sapiensGene 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
13Mus musculusGene Names: Ncoa2 (Grip1, Src2, Tif2)
Find proteins for Q61026 (Mus musculus)
Go to UniProtKB:  Q61026
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EES
Query on EES

Download SDF File 
Download CCD File 
A, B
3-CHLORO-2-(4-HYDROXYPHENYL)-2H-INDAZOL-5-OL
C13 H9 Cl N2 O2
ZNHQDSBJVFFIAK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 56.053α = 90.00
b = 84.266β = 108.48
c = 58.213γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
REFMACrefinement
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2017-10-18
    Type: Refinement description