2E2R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
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This is version 1.2 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 142: 517-524

  • DOI: https://doi.org/10.1093/jb/mvm158
  • Primary Citation of Related Structures:  
    2E2R

  • 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 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
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Estrogen-related receptor gamma244Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62508 (Homo sapiens)
Explore P62508 
Go to UniProtKB:  P62508
PHAROS:  P62508
GTEx:  ENSG00000196482 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62508
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.046α = 90
b = 64.046β = 90
c = 136.871γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
BBSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.2: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary