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 9W12 | pdb_00009w12

Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with ZOL-P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.197 (Depositor), 0.203 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.168 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 

Literature

A distinct zearalenone detoxification strategy mediated by cytochrome P450.

Liu, Z., Peng, R., Li, Q., Chen, C.C., Xin, L., Li, K., Huang, J.W., Liu, X., Zhang, X., Hu, L., Luo, S., Zhou, H., Li, A., Min, J., Guo, R.T.

(2026) Food Chem 510: 148697-148697

  • DOI: https://doi.org/10.1016/j.foodchem.2026.148697
  • Primary Citation Related Structures: 
    9W11, 9W12, 9W13

  • PubMed Abstract: 

    Developing the bio-detoxification of estrogenic mycotoxin zearalenone (ZEN) and its more potent metabolite α-zearalenol (α-ZOL) represents a research priority in food safety. Here, we report a variant cytochrome P450 enzyme termed T8F3 that consumes 54% ZEN and 63.9% α-ZOL in an initial screening assay. The hydroxylated products of ZEN and α-ZOL, termed ZEN-P and ZOL-P, respectively, were isolated, purified and structurally characterized. The estrogenicity of ZEN-P and ZOL-P is suppressed by 21- and 105-fold, respectively, compared with their parental compounds. Structural elucidation shows that T8F3-catalyzed hydroxylation at β-C8' (ZEN) and α-C3' (α-ZOL) positions, which might introduce steric hinderance that compromises the binding to estrogen receptor α, establishing a structure-detoxification relationship. Altogether, our study reports the first P450-mediated hydroxylation of ZEN and α-ZOL, resolves the mechanism of detoxification and addresses the behaviors of the hydroxylated ZEN and α-ZOL. These results should offer novel bio-detoxification machineries toward ZEN and derivatives.


  • Organizational Affiliation: 
    • School of Life Sciences, Hubei University, Wuhan 430062, PR China; Zhejiang Key Laboratory of Medical Epigenetics, Hubei Hongshan Laboratory, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, PR China.

Macromolecule Content 

  • Total Structure Weight: 60.53 kDa 
  • Atom Count: 4,270 
  • Modeled Residue Count: 497 
  • Deposited Residue Count: 526 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Estrogen receptor
A, B
263Homo sapiensMutation(s): 1 
Gene Names: ESR1, ESR, NR3A1
UniProt & NIH Common Fund Data Resources
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
PHAROS:  P03372
GTEx:  ENSG00000091831 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03372
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ET8
(Subject of Investigation/LOI)

Query on A1ET8



Download:Ideal Coordinates CCD File
C [auth A],
E [auth B]
(4S,8S,11S,12E)-4-methyl-8,11,16,18-tetrakis(oxidanyl)-3-oxabicyclo[12.4.0]octadeca-1(14),12,15,17-tetraen-2-one
C18 H24 O6
NCXPTKPSQNXPKF-ILBBBIAVSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
D [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
J [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth B],
G [auth B],
H [auth B],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.197 (Depositor), 0.203 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.168 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.753α = 90
b = 102.43β = 90
c = 195.933γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
SAINTdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-09-30
    Changes: Database references