2ZAS | pdb_00002zas

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with 4-alpha-cumylphenol, a bisphenol A derivative

• PDB DOI: https://doi.org/10.2210/pdb2ZAS/pdb

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


• Deposited: 2007-10-09 Released: 2008-10-07 
• Deposition Author(s): Matsushima, A., Kakuta, Y., Teramoto, T., Shimohigashi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

ERRgamma tethers strongly bisphenol A and 4-alpha-cumylphenol in an induced-fit manner

Matsushima, A., Teramoto, T., Okada, H., Liu, X., Tokunaga, T., Kakuta, Y., Shimohigashi, Y.

(2008) Biochem Biophys Res Commun 373: 408-413

• PubMed: 18582436 
• DOI: https://doi.org/10.1016/j.bbrc.2008.06.050
• Primary Citation of Related Structures:  
  2ZAS, 2ZBS


• PubMed Abstract: 
  

  A receptor-binding assay and X-ray crystal structure analysis demonstrated that the endocrine disruptor bisphenol A (BPA) strongly binds to human estrogen-related receptor gamma (ERRgamma). BPA is well anchored to the ligand-binding pocket, forming hydrogen bonds with its two phenol-hydroxyl groups. In this study, we found that 4-alpha-cumylphenol lacking one of its phenol-hydroxyl groups also binds to ERRgamma very strongly. The 2.0 A crystal structure of the 4-alpha-cumylphenol/ERRgamma complex clearly revealed that ERRgamma's Leu345-beta-isopropyl plays a role in the tight binding of 4-alpha-cumylphenol and BPA, rotating in a back-and-forth induced-fit manner.

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Organizational Affiliation: 

Laboratory of Structure-Function Biochemistry, Department of Chemistry, The Research-Education Centre of Risk Science, Faculty and Graduate School of Sciences, Kyushu University, Fukuoka 812-8581, Japan.

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: 27.92 kDa 
• Atom Count: 2,041 
• Modelled Residue Count: 227 
• Deposited Residue Count: 244 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Estrogen-related receptor gamma	A	244	Homo sapiens	Mutation(s): 0
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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1OH	B [auth A]	4-(1-methyl-1-phenylethyl)phenol C15 H16 O QBDSZLJBMIMQRS-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1OH	BindingDB:  2ZAS	IC50: 13.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.237 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.018	α = 90
b = 64.018	β = 90
c = 136.197	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Matsushima, A., Kakuta, Y., Teramoto, T., Shimohigashi, Y.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary