2E2R

Crystal structure of human estrogen-related receptor gamma ligand binding domain complex with bisphenol A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Evidence for Endocrine Disruptor Bisphenol A Binding to Human Nuclear Receptor ERR{gamma}

Matsushima, A.Kakuta, Y.Teramoto, T.Koshiba, T.Liu, X.Okada, H.Tokunaga, T.Kawabata, S.Kimura, M.Shimohigashi, Y.

(2007) J.Biochem.(Tokyo) 142: 517-524

  • DOI: 10.1093/jb/mvm158

  • PubMed Abstract: 
  • Many lines of evidence reveal that bisphenol A (BPA) functions at very low doses as an endocrine disruptor. The human estrogen-related receptor gamma (ERR gamma) behaves as a constitutive activator of transcription, although the endogenous ligand is ...

    Many lines of evidence reveal that bisphenol A (BPA) functions at very low doses as an endocrine disruptor. The human estrogen-related receptor gamma (ERR gamma) behaves as a constitutive activator of transcription, although the endogenous ligand is unknown. We have recently demonstrated that BPA binds strongly to ERR gamma (K(D) = 5.5 nM), but not to the estrogen receptor (ER). BPA preserves the ERR gamma's basal constitutive activity, and protects the selective ER modulator 4-hydroxytamoxifen from its deactivation of ERR gamma. In order to shed light on a molecular mechanism, we carried out the X-ray analysis of crystal structure of the ERR gamma ligand-binding domain (LBD) complexed with BPA. BPA binds to the receptor cavity without changing any internal structures of the pocket of the ERR gamma-LBD apo form. The hydrogen bonds of two phenol-hydroxyl groups, one with both Glu275 and Arg316, the other with Asn346, anchor BPA in the pocket, and surrounding hydrophobic bonds, especially with Tyr326, complete BPA's strong binding. Maintaining the 'activation helix' (helix 12) in an active conformation would as a result preserve receptor constitutive activity. Our results present the first evidence that the nuclear receptor forms complexes with the endocrine disruptor, providing detailed molecular insight into the interaction features.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Estrogen-related receptor gamma
A
244Homo sapiensMutation(s): 0 
Gene Names: ESRRG (ERR3, ERRG2, KIAA0832, NR3B3)
Find proteins for P62508 (Homo sapiens)
Go to Gene View: ESRRG
Go to UniProtKB:  P62508
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
2OH
Query on 2OH

Download SDF File 
Download CCD File 
A
4,4'-PROPANE-2,2-DIYLDIPHENOL
4,4'-ISOPROPYLIDENEDIPHENOL, BISPHENOL A
C15 H16 O2
IISBACLAFKSPIT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2OHIC50: 13.1 nM (99) BINDINGDB
2OHKd: 5.5 nM BINDINGMOAD
2OHKd: 5.5 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.046α = 90.00
b = 64.046β = 90.00
c = 136.871γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
BBSdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance