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 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.03 kDa 
• Atom Count: 1893 
• Modelled Residue Count: 227 
• Deposited Residue Count: 227 
• Unique protein chains: 1

6K3N

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with BPA-monoF

• PDB DOI: 10.2210/pdb6K3N/pdb

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


• Deposited: 2019-05-21 Released: 2020-05-13 
• Deposition Author(s): Matsushima, A., Nose, T., Kakuta, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Literature

Evaluation of the Influence of Halogenation on the Binding of Bisphenol A to the Estrogen-Related Receptor gamma.

Suyama, K., Kaneko, S., Kesamaru, H., Liu, X., Matsushima, A., Kakuta, Y., Okubo, T., Kasatani, K., Nose, T.

(2020) Chem Res Toxicol 33: 889-902

• PubMed: 32105061 
• DOI: 10.1021/acs.chemrestox.9b00379
• Primary Citation of Related Structures:  
  6K3N


• PubMed Abstract: 
  

Halogenation of organic compounds is one the most important transformations in chemical synthesis and is used for the production of various industrial products. A variety of halogenated bisphenol analogs have recently been developed and are used as alternatives to bisphenol A (BPA), which is a raw material of polycarbonate that has adverse effects in animals. However, limited information is available on the potential toxicity of the halogenated BPA analogs. In the present study, to assess the latent toxicity of halogenated BPA analogs, we evaluated the binding and transcriptional activities of halogenated BPA analogs to the estrogen-related receptor γ (ERRγ), a nuclear receptor that contributes to the growth of nerves and sexual glands. Fluorinated BPA analogs demonstrated strong ERRγ binding potency, and inverse antagonistic activity, similar to BPA. X-ray crystallography and fragment molecular orbital (FMO) calculation revealed that a fluorine-substituted BPA analog could interact with several amino acid residues of ERRγ-LBD, strengthening the binding affinity of the analogs. The ERRγ binding affinity and transcriptional activity of the halogenated BPAs decreased with the increase in the size and number of halogen atom(s). The IC ₅₀ values, determined by the competitive binding assay, correlated well with the binding energy obtained from the docking calculation, suggesting that the docking calculation could correctly estimate the ERRγ binding potency of the BPA analogs. These results confirmed that ERRγ has a ligand binding pocket that fits very well to BPA. Furthermore, this study showed that the binding affinity of the BPA analogs can be predicted by the docking calculation, indicating the importance of the calculation method in the risk assessment of halogenated compounds.

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Organizational Affiliation: 

Department of Chemistry, Faculty and Graduate School of Science, Fukuoka 819-0395, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A	227	Homo sapiens	Mutation(s): 0  Gene Names: ESRRG, ERR3, ERRG2, KIAA0832, NR3B3
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens) Explore P62508  Go to UniProtKB:  P62508
PHAROS:  P62508 GTEx:  ENSG00000196482

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CW6 (Subject of Investigation/LOI)	B [auth A]	2-fluoranyl-4-[2-(4-hydroxyphenyl)propan-2-yl]phenol C15 H15 F O2 XMEGCBLYVCFWLJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
CW6	Binding MOAD:  6K3N	IC50: 5.3 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.253 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.666	α = 90
b = 63.666	β = 90
c = 132.212	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2019-05-21 
• Released Date: 2020-05-13 
Deposition Author(s): Matsushima, A., Nose, T., Kakuta, Y.

Revision History  

• Version 1.0: 2020-05-13
  Type: Initial release