Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 29.00 kDa 
• Atom Count: 1991 
• Modelled Residue Count: 230 
• Deposited Residue Count: 255 
• Unique protein chains: 1

1QKM

HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN

• PDB DOI: 10.2210/pdb1QKM/pdb

• Classification: NUCLEAR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-07-27 Released: 2000-07-28 
• Deposition Author(s): Pike, A.C.W., Brzozowski, A.M., Carlquist, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.215 

Literature

Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist

Pike, A.C.W., Brzozowski, A.M., Hubbard, R.E., Bonn, T., Thorsell, A.-G., Engstrom, O., Ljunggren, J., Gustaffson, J.-A., Carlquist, M.

(1999) EMBO J 18: 4608

• PubMed: 10469641 
• DOI: 10.1093/emboj/18.17.4608
• Primary Citation of Related Structures:  
  1QKM, 1QKN


• PubMed Abstract: 
  

Oestrogens exert their physiological effects through two receptor subtypes. Here we report the three-dimensional structure of the oestrogen receptor beta isoform (ERbeta) ligand-binding domain (LBD) in the presence of the phyto-oestrogen genistein and the antagonist raloxifene. The overall structure of ERbeta-LBD is very similar to that previously reported for ERalpha. Each ligand interacts with a unique set of residues within the hormone-binding cavity and induces a distinct orientation in the AF-2 helix (H12). The bulky side chain of raloxifene protrudes from the cavity and physically prevents the alignment of H12 over the bound ligand. In contrast, genistein is completely buried within the hydrophobic core of the protein and binds in a manner similar to that observed for ER's endogenous hormone, 17beta-oestradiol. However, in the ERbeta-genistein complex, H12 does not adopt the distinctive 'agonist' position but, instead, lies in a similar orientation to that induced by ER antagonists. Such a sub-optimal alignment of the transactivation helix is consistent with genistein's partial agonist character in ERbeta and demonstrates how ER's transcriptional response to certain bound ligands is attenuated.

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Related Citations: 

• Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor
  Brzozowski, A.M., Pike, A.C.W., Dauter, Z., Hubbard, R.E., Bonn, T., Engstrom, O., Ohman, L., Greene, G.L., Gustaffson, J.-A., Carlquist, M.
  (1997) Nature 389: 753

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Organizational Affiliation: 

Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5DD, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR BETA	A	255	Homo sapiens	Mutation(s): 0  Gene Names: OESTROGEN RECEPTOR BETA, ESR2, ESTRB, NR3A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92731 (Homo sapiens) Explore Q92731  Go to UniProtKB:  Q92731
PHAROS:  Q92731 GTEx:  ENSG00000140009

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
GEN	BindingDB:  1QKM	Ki: 24 (nM) from 1 assay(s)
		IC50: min: 1.3, max: 990 (nM) from 14 assay(s)
		EC50: min: 2.4, max: 200 (nM) from 6 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.252 
• R-Value Work: 0.215 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.12	α = 90
b = 63.12	β = 90
c = 250.23	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-07-27 
• Released Date: 2000-07-28 
Deposition Author(s): Pike, A.C.W., Brzozowski, A.M., Carlquist, M.

Revision History  

• Version 1.0: 2000-07-28
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance