Biological Assembly 1  

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

Global Symmetry: Cyclic - C2  (3D View)
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: 62.79 kDa 
• Atom Count: 4277 
• Modelled Residue Count: 503 
• Deposited Residue Count: 540 
• Unique protein chains: 2

1ZKY

Human Estrogen Receptor Alpha Ligand-Binding Domain In Complex With OBCP-3M and A Glucocorticoid Receptor Interacting Protein 1 Nr Box II Peptide

• PDB DOI: 10.2210/pdb1ZKY/pdb

• Classification: HORMONE/GROWTH FACTOR RECEPTOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-05-04 Released: 2006-05-09 
• Deposition Author(s): Rajan, S.S., Hsieh, R.W., Sharma, S.K., Hahm, J.B., Nettles, K.W., Greene, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 

Literature

Identification of ligands with bicyclic scaffolds provides insights into mechanisms of estrogen receptor subtype selectivity.

Hsieh, R.W., Rajan, S.S., Sharma, S.K., Guo, Y., Desombre, E.R., Mrksich, M., Greene, G.L.

(2006) J Biol Chem 281: 17909-17919

• PubMed: 16648639 
• DOI: 10.1074/jbc.M513684200
• Primary Citation of Related Structures:  
  1ZKY, 2B1V, 2FAI


• PubMed Abstract: 
  

Estrogen receptors alpha (ERalpha) and beta (ERbeta) have distinct functions and differential expression in certain tissues. These differences have stimulated the search for subtype-selective ligands. Therapeutically, such ligands offer the potential to target specific tissues or pathways regulated by one receptor subtype without affecting the other. As reagents, they can be utilized to probe the physiological functions of the ER subtypes to provide information complementary to that obtained from knock-out animals. A fluorescence resonance energy transfer-based assay was used to screen a 10,000-compound chemical library for ER agonists. From the screen, we identified a family of ERbeta-selective agonists whose members contain bulky oxabicyclic scaffolds in place of the planar scaffolds common to most ER ligands. These agonists are 10-50-fold selective for ERbeta in competitive binding assays and up to 60-fold selective in transactivation assays. The weak uterotrophic activity of these ligands in immature rats and their ability to stimulate expression of an ERbeta regulated gene in human U2OS osteosarcoma cells provides more physiological evidence of their ERbeta-selective nature. To provide insight into the molecular mechanisms of their activity and selectivity, we determined the crystal structures of the ERalpha ligand-binding domain (LBD) and a peptide from the glucocorticoid receptor-interacting protein 1 (GRIP1) coactivator complexed with the ligands OBCP-3M, OBCP-2M, and OBCP-1M. These structures illustrate how the bicyclic scaffolds of these ligands are accommodated in the flexible ligand-binding pocket of ER. A comparison of these structures with existing ER structures suggests that the ERbeta selectivity of OBCP ligands can be attributed to a combination of their interactions with Met-336 in ERbeta and Met-421 in ERalpha. These bicyclic ligands show promise as lead compounds that can target ERbeta. In addition, our understanding of the molecular determinants of their subtype selectivity provides a useful starting point for developing other ER modulators belonging to this relatively new structural class.

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Organizational Affiliation: 

Ben May Institute for Cancer Research, University of Chicago W330, 929 E. 57th Street, Chicago, IL 60637, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen receptor	A, B	257	Homo sapiens	Mutation(s): 4  Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 2	C, D	13	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
689	E [auth A], F [auth B]	4-[(1S,2S,5S)-5-(HYDROXYMETHYL)-6,8,9-TRIMETHYL-3-OXABICYCLO[3.3.1]NON-7-EN-2-YL]PHENOL C18 H24 O3 DTZWKYVREFMAJA-QXWBOSQLSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CME	A, B	L-PEPTIDE LINKING	C5 H11 N O3 S2		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
689	Binding MOAD:  1ZKY	Ki: 560 (nM) from 1 assay(s)
	PDBBind:  1ZKY	Ki: 560 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.231 
• R-Value Work: 0.185 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.929	α = 90
b = 84.129	β = 109.06
c = 58.22	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-05-04 
• Released Date: 2006-05-09 
Deposition Author(s): Rajan, S.S., Hsieh, R.W., Sharma, S.K., Hahm, J.B., Nettles, K.W., Greene, G.L.

Revision History  

• Version 1.0: 2006-05-09
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations