1X7J

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH GENISTEIN

• PDB DOI: https://doi.org/10.2210/pdb1X7J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-08-14 Released: 2005-03-01 
• Deposition Author(s): Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Understanding the Selectivity of Genistein for Human Estrogen Receptor-Beta Using X-Ray Crystallography and Computational Methods

Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

(2004) Structure 12: 2197-2207

• PubMed: 15576033 
• DOI: https://doi.org/10.1016/j.str.2004.09.015
• Primary Citation of Related Structures:  
  1X7J, 1X7R


• PubMed Abstract: 
  

  We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha. In addition, we examine subtle differences between binding site residues, providing an explanation for why genistein is modestly selective for the beta isoform. To this end, we also present the results of quantum chemical studies and thermodynamic arguments that yield insight to the nature of the interactions leading to estrogen receptor-beta selectivity. The importance of our analysis to structure-based drug design is discussed.

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Organizational Affiliation: 

Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, PA 19426, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.53 kDa 
• Atom Count: 3,832 
• Modelled Residue Count: 470 
• Deposited Residue Count: 506 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor beta	A, B	240	Homo sapiens	Mutation(s): 0  Gene Names: ESR2, NR3A2, ESTRB
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
STEROID RECEPTOR COACTIVATOR-1	C, D	13	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GEN	E [auth A], F [auth B]	GENISTEIN C15 H10 O5 TZBJGXHYKVUXJN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GEN	BindingDB:  1X7J	Ki: 24 (nM) from 1 assay(s)
		IC50: min: 1.3, max: 990 (nM) from 15 assay(s)
		EC50: min: 2.4, max: 200 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 
• R-Value Observed: 0.236 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.231	α = 90
b = 87.667	β = 90
c = 100.113	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-01 
Deposition Author(s): Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

Revision History  

• Version 1.0: 2005-03-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description