1QKU

WILD TYPE ESTROGEN NUCLEAR RECEPTOR LIGAND BINDING DOMAIN COMPLEXED WITH ESTRADIOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a mutant hERalpha ligand-binding domain reveals key structural features for the mechanism of partial agonism.

Gangloff, M.Ruff, M.Eiler, S.Duclaud, S.Wurtz, J.M.Moras, D.

(2001) J Biol Chem 276: 15059-15065

  • DOI: 10.1074/jbc.M009870200
  • Primary Citation of Related Structures:  
    1QKU, 1QKT

  • PubMed Abstract: 
  • The crystal structure of a triple cysteine to serine mutant ERalpha ligand-binding domain (LBD), complexed with estradiol, shows that despite the presence of a tightly bound agonist ligand, the protein exhibits an antagonist-like conformation, similar to that observed in raloxifen and 4-hydroxytamoxifen-bound structures ...

    The crystal structure of a triple cysteine to serine mutant ERalpha ligand-binding domain (LBD), complexed with estradiol, shows that despite the presence of a tightly bound agonist ligand, the protein exhibits an antagonist-like conformation, similar to that observed in raloxifen and 4-hydroxytamoxifen-bound structures. This mutated receptor binds estradiol with wild type affinity and displays transcriptional activity upon estradiol stimulation, but with limited potency (about 50%). This partial activity is efficiently repressed in antagonist competition assays. The comparison with available LBD structures reveals key features governing the positioning of helix H12 and highlights the importance of cysteine residues in promoting an active conformation. Furthermore the present study reveals a hydrogen bond network connecting ligand binding to protein trans conformation. These observations support a dynamic view of H12 positioning, where the control of the equilibrium between two stable locations determines the partial agonist character of a given ligand.


    Organizational Affiliation

    Institut de Genetique et de Biologie Moleculaire et Cellulaire, Laboratoire de Biologie et de Génomique Structurales 1, rue Laurent Fries, BP 163 67404 Illkirch, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ESTRADIOL RECEPTOR ABC250Homo sapiensMutation(s): 0 
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
EST
Query on EST

Download Ideal Coordinates CCD File 
A, B, C
ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESTKi:  100   nM  BindingDB
ESTIC50:  5.699999809265137   nM  BindingDB
ESTEC50:  0.75   nM  BindingDB
ESTIC50:  4.699999809265137   nM  BindingDB
ESTEC50:  1   nM  BindingDB
ESTIC50:  3.5999999046325684   nM  BindingDB
ESTIC50:  0.3499999940395355   nM  BindingDB
ESTEC50:  0   nM  BindingDB
ESTIC50:  3.200000047683716   nM  BindingDB
ESTEC50:  0.3700000047683716   nM  BindingDB
ESTIC50:  1.350000023841858   nM  BindingDB
ESTIC50:  1.600000023841858   nM  BindingDB
ESTKi:  0.14000000059604645   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTEC50:  0.3100000023841858   nM  BindingDB
ESTEC50:  3.799999952316284   nM  BindingDB
ESTKi:  0.8299999833106995   nM  BindingDB
ESTEC50:  0.019999999552965164   nM  BindingDB
ESTIC50:  1.7999999523162842   nM  BindingDB
ESTKi:  12   nM  BindingDB
ESTIC50:  5.900000095367432   nM  BindingDB
ESTIC50:  4.400000095367432   nM  BindingDB
ESTEC50:  1.0499999523162842   nM  BindingDB
ESTIC50:  0.44999998807907104   nM  BindingDB
ESTIC50:  1.2999999523162842   nM  BindingDB
ESTEC50:  0.07999999821186066   nM  BindingDB
ESTIC50:  2.200000047683716   nM  BindingDB
ESTEC50:  0.10999999940395355   nM  BindingDB
ESTKi:  2   nM  BindingDB
ESTIC50:  0.8999999761581421   nM  BindingDB
ESTEC50:  0.25999999046325684   nM  BindingDB
ESTKi:  0.20999999344348907   nM  BindingDB
ESTKi:  0.18000000715255737   nM  BindingDB
ESTKi:  0.30000001192092896   nM  BindingDB
ESTEC50:  0.1599999964237213   nM  BindingDB
ESTKi:  0.11999999731779099   nM  BindingDB
ESTEC50:  3.200000047683716   nM  BindingDB
ESTIC50:  2   nM  BindingDB
ESTEC50:  2.200000047683716   nM  BindingDB
ESTIC50:  0.10999999940395355   nM  BindingDB
ESTIC50:  3.4000000953674316   nM  BindingDB
ESTEC50:  0.28999999165534973   nM  BindingDB
ESTEC50:  0.11999999731779099   nM  BindingDB
ESTEC50:  0.09000000357627869   nM  BindingDB
ESTKi:  0.10999999940395355   nM  BindingDB
ESTIC50:  1.2000000476837158   nM  BindingDB
ESTEC50:  1.100000023841858   nM  BindingDB
ESTKi:  0.1599999964237213   nM  BindingDB
ESTIC50:  0.5   nM  BindingDB
ESTIC50:  1.7000000476837158   nM  BindingDB
ESTIC50:  0.75   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTIC50:  1   nM  BindingDB
ESTEC50:  0.15000000596046448   nM  BindingDB
ESTEC50:  0.029999999329447746   nM  BindingDB
ESTEC50:  0.699999988079071   nM  BindingDB
ESTIC50:  1.5   nM  BindingDB
ESTKd:  3   nM  BindingDB
ESTEC50:  2.299999952316284   nM  BindingDB
ESTIC50:  2   nM  BindingDB
ESTEC50:  0.5600000023841858   nM  BindingDB
ESTEC50:  0.009999999776482582   nM  BindingDB
ESTEC50:  0.20000000298023224   nM  BindingDB
ESTIC50:  3   nM  BindingDB
ESTKd:  100   nM  BindingDB
ESTIC50:  1.399999976158142   nM  BindingDB
ESTIC50:  4   nM  BindingDB
ESTEC50:  0.07000000029802322   nM  BindingDB
ESTEC50:  0.10000000149011612   nM  BindingDB
ESTEC50:  0.49000000953674316   nM  BindingDB
ESTIC50:  21.040000915527344   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTIC50:  11   nM  BindingDB
ESTIC50:  0.009999999776482582   nM  BindingDB
ESTIC50:  10   nM  BindingDB
ESTEC50:  0.05000000074505806   nM  BindingDB
ESTEC50:  2.7699999809265137   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTKi:  0.6499999761581421   nM  BindingDB
ESTIC50:  12.5   nM  BindingDB
ESTEC50:  0.18000000715255737   nM  BindingDB
ESTIC50:  0.5699999928474426   nM  BindingDB
ESTIC50:  18   nM  BindingDB
ESTEC50:  3   nM  BindingDB
ESTEC50:  2.4000000953674316   nM  BindingDB
ESTKd:  0.20000000298023224   nM  BindingDB
ESTIC50:  0.8199999928474426   nM  BindingDB
ESTEC50:  0.47999998927116394   nM  BindingDB
ESTIC50:  24   nM  BindingDB
ESTIC50:  4.800000190734863   nM  BindingDB
ESTIC50:  28   nM  BindingDB
ESTKd :  0.25999999046325684   nM  PDBBind
ESTKi:  2.200000047683716   nM  BindingDB
ESTIC50:  0.699999988079071   nM  BindingDB
ESTEC50:  0.5899999737739563   nM  BindingDB
ESTIC50:  46   nM  BindingDB
ESTEC50:  10   nM  BindingDB
ESTIC50:  0.4099999964237213   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.5α = 90
b = 105.5β = 90
c = 136.08γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-18
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Database references, Source and taxonomy