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- PDB-9w11: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) i... -

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Basic information

Entry
Database: PDB / ID: 9w11
TitleCrystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with beta-zearalenol
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / beta-zearalenol / ER-alpha
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / regulation of toll-like receptor signaling pathway / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / steroid hormone receptor signaling pathway / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / nuclear estrogen receptor activity / regulation of toll-like receptor signaling pathway / prostate epithelial cord elongation / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell development / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / negative regulation of smooth muscle cell apoptotic process / nuclear receptor-mediated steroid hormone signaling pathway / mammary gland alveolus development / : / cellular response to estrogen stimulus / estrogen response element binding / : / Mitochondrial unfolded protein response (UPRmt) / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / protein localization to chromatin / 14-3-3 protein binding / ESR-mediated signaling / negative regulation of miRNA transcription / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / negative regulation of canonical NF-kappaB signal transduction / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / Nuclear Receptor transcription pathway / response to estrogen / beta-catenin binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / transcription coactivator binding / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Regulation of RUNX2 expression and activity / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / phospholipase C-activating G protein-coupled receptor signaling pathway / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / protein kinase binding / positive regulation of DNA-templated transcription / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Chem-ZHB / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsPeng, R.M. / Min, J. / Li, K.K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal Structure of the ER-alpha Ligand-binding Domain (Y537S) in Complex with beta-zearalenol
Authors: Peng, R.M. / Min, J. / Li, K.K.
History
DepositionJul 25, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4038
Polymers59,4022
Non-polymers1,0016
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-30 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.558, 102.254, 196.003
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-870-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 29700.951 Da / Num. of mol.: 2 / Mutation: Y537S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372

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Non-polymers , 5 types, 221 molecules

#2: Chemical ChemComp-ZHB / (3S,7S,11E)-7,14,16-trihydroxy-3-methyl-3,4,5,6,7,8,9,10-octahydro-1H-2-benzoxacyclotetradecin-1-one


Mass: 320.380 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 18% (w/v) PEG 3350, 0.25 M Ammonium sulfate, and 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: LIQUID ANODE / Type: BRUKER METALJET / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: Jun 20, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.83→25 Å / Num. obs: 45136 / % possible obs: 96.2 % / Redundancy: 5 % / CC1/2: 0.993 / Net I/σ(I): 25.81
Reflection shellResolution: 1.83→1.9 Å / Num. unique obs: 4571 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SAINTdata scaling
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.83→24.75 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.995 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22573 2194 4.9 %RANDOM
Rwork0.17919 ---
obs0.18135 42900 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.986 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å2-0 Å20 Å2
2--1.53 Å20 Å2
3----2.21 Å2
Refinement stepCycle: 1 / Resolution: 1.83→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 67 215 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134075
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173966
X-RAY DIFFRACTIONr_angle_refined_deg1.641.6345497
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5889185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7385491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4722.188192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96715766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9221524
X-RAY DIFFRACTIONr_chiral_restr0.0970.2521
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024363
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8833.3111976
X-RAY DIFFRACTIONr_mcbond_other2.8783.3091975
X-RAY DIFFRACTIONr_mcangle_it3.7764.9382460
X-RAY DIFFRACTIONr_mcangle_other3.7754.942461
X-RAY DIFFRACTIONr_scbond_it4.2143.8662099
X-RAY DIFFRACTIONr_scbond_other4.2133.8672100
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2565.6033037
X-RAY DIFFRACTIONr_long_range_B_refined7.54740.2224641
X-RAY DIFFRACTIONr_long_range_B_other7.52740.0824599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.832→1.879 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 166 -
Rwork0.232 3166 -
obs--97.06 %

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