2P15

Crystal structure of the ER alpha ligand binding domain with the agonist ortho-trifluoromethylphenylvinyl estradiol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural plasticity in the oestrogen receptor ligand-binding domain.

Nettles, K.W.Bruning, J.B.Gil, G.O'Neill, E.E.Nowak, J.Guo, Y.Kim, Y.DeSombre, E.R.Dilis, R.Hanson, R.N.Joachimiak, A.Greene, G.L.

(2007) EMBO Rep 8: 563-568

  • DOI: 10.1038/sj.embor.7400963
  • Primary Citation of Related Structures:  
    2P15

  • PubMed Abstract: 
  • The steroid hormone receptors are characterized by binding to relatively rigid, inflexible endogenous steroid ligands. Other members of the nuclear receptor superfamily bind to conformationally flexible lipids and show a corresponding degree of elasticity in the ligand-binding pocket ...

    The steroid hormone receptors are characterized by binding to relatively rigid, inflexible endogenous steroid ligands. Other members of the nuclear receptor superfamily bind to conformationally flexible lipids and show a corresponding degree of elasticity in the ligand-binding pocket. Here, we report the X-ray crystal structure of the oestrogen receptor alpha (ERalpha) bound to an oestradiol derivative with a prosthetic group, ortho- trifluoromethlyphenylvinyl, which binds in a novel extended pocket in the ligand-binding domain. Unlike ER antagonists with bulky side groups, this derivative is enclosed in the ligand-binding pocket, and acts as a potent agonist. This work shows that steroid hormone receptors can interact with a wider array of pharmacophores than previously thought through structural plasticity in the ligand-binding pocket.


    Organizational Affiliation

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



Macromolecules
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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
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
GRIP peptideC, D13N/AMutation(s): 0 
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
NIH Common Fund Data Resources
PHAROS:  Q15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EZT
Query on EZT

Download Ideal Coordinates CCD File 
E [auth A], F [auth B](17BETA)-17-{(E)-2-[2-(TRIFLUOROMETHYL)PHENYL]VINYL}ESTRA-1(10),2,4-TRIENE-3,17-DIOL
C27 H29 F3 O2
WSMPLUQFTPBNJI-NYFISDDFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
EZTKd :  0.05000000074505806   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.052α = 90
b = 84.22β = 109.59
c = 58.693γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description