2QXS

Crystal Structure of Antagonizing Mutant 536S of the Estrogen Receptor Alpha Ligand Binding Domain Complexed to Raloxifene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Coupling of receptor conformation and ligand orientation determine graded activity.

Bruning, J.B.Parent, A.A.Gil, G.Zhao, M.Nowak, J.Pace, M.C.Smith, C.L.Afonine, P.V.Adams, P.D.Katzenellenbogen, J.A.Nettles, K.W.

(2010) Nat Chem Biol 6: 837-843

  • DOI: 10.1038/nchembio.451
  • Primary Citation of Related Structures:  
    2QXS, 2QZO, 3OSA, 3OS8, 3OS9

  • PubMed Abstract: 
  • Small molecules stabilize specific protein conformations from a larger ensemble, enabling molecular switches that control diverse cellular functions. We show here that the converse also holds true: the conformational state of the estrogen receptor can direct distinct orientations of the bound ligand ...

    Small molecules stabilize specific protein conformations from a larger ensemble, enabling molecular switches that control diverse cellular functions. We show here that the converse also holds true: the conformational state of the estrogen receptor can direct distinct orientations of the bound ligand. 'Gain-of-allostery' mutations that mimic the effects of ligand in driving protein conformation allowed crystallization of the partial agonist ligand WAY-169916 with both the canonical active and inactive conformations of the estrogen receptor. The intermediate transcriptional activity induced by WAY-169916 is associated with the ligand binding differently to the active and inactive conformations of the receptor. Analyses of a series of chemical derivatives demonstrated that altering the ensemble of ligand binding orientations changes signaling output. The coupling of different ligand binding orientations to distinct active and inactive protein conformations defines a new mechanism for titrating allosteric signaling activity.


    Organizational Affiliation

    Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, Florida, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA, B258Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS:  P03372
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAL
Query on RAL

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]RALOXIFENE
C28 H27 N O4 S
GZUITABIAKMVPG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, BL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RALIC50:  0.20000000298023224   nM  BindingDB
RALIC50:  1.7999999523162842   nM  BindingDB
RALEC50:  2.4000000953674316   nM  BindingDB
RALKi:  2   nM  BindingDB
RALKi:  0.4300000071525574   nM  BindingDB
RALIC50:  22   nM  BindingDB
RALIC50:  0.699999988079071   nM  BindingDB
RALIC50:  0.4699999988079071   nM  BindingDB
RALIC50:  24   nM  BindingDB
RALIC50:  0.699999988079071   nM  BindingDB
RALIC50:  0.30000001192092896   nM  BindingDB
RALKi:  0.3799999952316284   nM  BindingDB
RALIC50:  20.600000381469727   nM  BindingDB
RALIC50:  0.46000000834465027   nM  BindingDB
RALIC50:  0.7300000190734863   nM  BindingDB
RALIC50:  2   nM  BindingDB
RALIC50:  7   nM  BindingDB
RALIC50:  7.699999809265137   nM  BindingDB
RALKi:  0.2199999988079071   nM  BindingDB
RALIC50:  0.8899999856948853   nM  BindingDB
RALIC50:  1.899999976158142   nM  BindingDB
RALIC50:  4   nM  BindingDB
RALIC50:  7   nM  BindingDB
RALKi:  0.4000000059604645   nM  BindingDB
RALEC50:  22   nM  BindingDB
RALKi:  0.029999999329447746   nM  BindingDB
RALIC50:  0.3400000035762787   nM  BindingDB
RALIC50:  0.7200000286102295   nM  BindingDB
RALIC50:  222   nM  BindingDB
RALIC50:  170   nM  BindingDB
RALKi:  0.3700000047683716   nM  BindingDB
RALEC50:  4.320000171661377   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.588α = 90
b = 58.102β = 102.66
c = 87.95γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-10-25
    Changes: Advisory, Atomic model, Refinement description, Source and taxonomy