2YAT

Crystal structure of estradiol derived metal chelate and estrogen receptor-ligand binding domain complex

• PDB DOI: https://doi.org/10.2210/pdb2YAT/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-02-24 Released: 2011-06-01 
• Deposition Author(s): Li, M.J., Greenblatt, H.M., Dym, O., Albeck, S., Degani, H., Sussman, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Structure of Estradiol Metal Chelate and Estrogen Receptor Complex: The Basis for Designing a New Class of Selective Estrogen Receptor Modulators.

Li, M.J., Greenblatt, H.M., Dym, O., Albeck, S., Pais, A., Gunanathan, C., Milstein, D., Degani, H., Sussman, J.L.

(2011) J Med Chem 54: 3575

• PubMed: 21473635 
• DOI: https://doi.org/10.1021/jm200192y
• Primary Citation of Related Structures:  
  2YAT


• PubMed Abstract: 
  

  Selective estrogen receptor modulators, such as 17β-estradiol derivatives bound to metal complexes, have been synthesized as targeted probes for the diagnosis and treatment of breast cancer. Here, we report the detailed 3D structure of estrogen receptor α ligand-binding domain (ERα-LBD) bound with a novel estradiol-derived metal complex, estradiol-pyridine tetra acetate europium(III), at 2.6 Å resolution. This structure provides important information pertinent to the design of novel functional ERα targeted probes for clinical applications.

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Organizational Affiliation: 

Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 29.68 kDa 
• Atom Count: 1,894 
• Modelled Residue Count: 227 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ESTROGEN RECEPTOR	A	252	Homo sapiens	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens) Explore P03372  Go to UniProtKB:  P03372
PHAROS:  P03372 GTEx:  ENSG00000091831

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EEU	C [auth A]	ESTRADIOL-PYRIDINIUM TETRAACETIC ACID C35 H41 N3 O10 ASNZLCSGYOKOKE-MXUGPSOYSA-N
EU	B [auth A]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N
FMT	D [auth A], E [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.228 
• R-Value Work: 0.182 
• R-Value Observed: 0.184 
• Space Group: P 3₂ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.693	α = 90
b = 64.693	β = 90
c = 133.345	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-01 
Deposition Author(s): Li, M.J., Greenblatt, H.M., Dym, O., Albeck, S., Degani, H., Sussman, J.L.

Revision History  

• Version 1.0: 2011-06-01
  Type: Initial release
  
• Version 1.1: 2012-05-16
  Changes: Database references, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description