1A52

ESTROGEN RECEPTOR ALPHA LIGAND-BINDING DOMAIN COMPLEXED TO ESTRADIOL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystallographic comparison of the estrogen and progesterone receptor's ligand binding domains.

Tanenbaum, D.M., Wang, Y., Williams, S.P., Sigler, P.B.

(1998) Proc.Natl.Acad.Sci.USA 95: 5998-6003


  • PubMed Abstract: 

    • The 2.8-A crystal structure of the complex formed by estradiol and the human estrogen receptor-alpha ligand binding domain (hERalphaLBD) is described and compared with the recently reported structure of the progesterone complex of the human progester ...

    The 2.8-A crystal structure of the complex formed by estradiol and the human estrogen receptor-alpha ligand binding domain (hERalphaLBD) is described and compared with the recently reported structure of the progesterone complex of the human progesterone receptor ligand binding domain, as well as with similar structures of steroid/nuclear receptor LBDs solved elsewhere. The hormone-bound hERalphaLBD forms a distinctly different and probably more physiologically important dimer interface than its progesterone counterpart. A comparison of the specificity determinants of hormone binding reveals a common structural theme of mutually supported van der Waals and hydrogen-bonded interactions involving highly conserved residues. The previously suggested mechanism by which the estrogen receptor distinguishes estradiol's unique 3-hydroxy group from the 3-keto function of most other steroids is now described in atomic detail. Mapping of mutagenesis results points to a coactivator-binding surface that includes the region around the "signature sequence" as well as helix 12, where the ligand-dependent conformation of the activation function 2 core is similar in all previously solved steroid/nuclear receptor LBDs. A peculiar crystal packing event displaces helix 12 in the hERalphaLBD reported here, suggesting a higher degree of dynamic variability than expected for this critical substructure.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry and the Howard Hughes Medical Institute, Yale University, 260 Whitney Avenue, JWG 423, New Haven, CT 06511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ESTROGEN RECEPTOR
A, B
258Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AU
Query on AU
Download SDF File 
Download CCD File 
A, B
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
EST
Query on EST
Download SDF File 
Download CCD File 
A, B
ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESTIC50: 1.9 - 2.2 nM (94) BINDINGDB
ESTKi: 0.138 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.223 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 147.000α = 90.00
b = 147.000β = 90.00
c = 168.900γ = 120.00
Software Package:
Software NamePurpose
MLPHAREphasing
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model