6LIT

Estrogen-related receptor beta(ERR2) in complex with BPA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


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Literature

Structural Insights into the Specificity of Ligand Binding and Coactivator Assembly by Estrogen-Related Receptor beta.

Yao, B.Zhang, S.Wei, Y.Tian, S.Lu, Z.Jin, L.He, Y.Xie, W.Li, Y.

(2020) J Mol Biol 432: 5460-5472

  • DOI: 10.1016/j.jmb.2020.08.007
  • Primary Citation of Related Structures:  
    6LIT, 6LN4

  • PubMed Abstract: 
  • Estrogen-related receptor β (ERRβ) is a nuclear receptor critical for many biological processes. Despite the biological and pharmaceutical importance of ERRβ, deciphering the structure of ERRβ has been hampered by the difficulties in obtaining a pure and stable protein for structural studies ...

    Estrogen-related receptor β (ERRβ) is a nuclear receptor critical for many biological processes. Despite the biological and pharmaceutical importance of ERRβ, deciphering the structure of ERRβ has been hampered by the difficulties in obtaining a pure and stable protein for structural studies. In fact, the ERRβ ligand-binding domain remains the last unsolved ERR structure and also one of only a few unknown nuclear receptor structures. Here, we report the identification of a critical single-residue mutation resulted in robust solubility and stability of an active ERRβ ligand-binding domain, thereby providing a protein tool enabling the first probe into the biochemical and structural studies of this important receptor. The crystal structure reveals key structural features that have enabled the integration of the molecular determinants of signals transduced across the ligand binding and coregulator recruitment by all three ERR subtypes, which also provides a framework for the rational design of selective and potent ligands for the treatment of various ERR-mediated diseases.


    Organizational Affiliation

    The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China. Electronic address: yongli@xmu.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Steroid hormone receptor ERR2A, B230Homo sapiensMutation(s): 3 
Gene Names: ESRRBERRB2ESRL2NR3B2
UniProt & NIH Common Fund Data Resources
Find proteins for O95718 (Homo sapiens)
Explore O95718 
Go to UniProtKB:  O95718
PHAROS:  O95718
GTEx:  ENSG00000119715 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95718
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
10-mer from Nuclear receptor coactivator 2C [auth D],
D [auth E]
11Homo sapiensMutation(s): 0 
Gene Names: NCOA2BHLHE75SRC2TIF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens)
Explore Q15596 
Go to UniProtKB:  Q15596
PHAROS:  Q15596
GTEx:  ENSG00000140396 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15596
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2OH (Subject of Investigation/LOI)
Query on 2OH

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B]
4,4'-PROPANE-2,2-DIYLDIPHENOL
C15 H16 O2
IISBACLAFKSPIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.193 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.951α = 84.31
b = 45.027β = 80.02
c = 57.368γ = 79.31
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-12-13 
  • Released Date: 2020-10-07 
  • Deposition Author(s): Yao, B.Q., Li, Y.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770814

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release