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- PDB-7xvz: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 7xvz
TitleHuman Estrogen Receptor beta Ligand-binding Domain in Complex with (R)-3-(2-chloro-4-hydroxyphenyl)-2-(4-hydroxyphenyl)propanenitrile
Components
  • Estrogen receptor beta
  • SRC peptide
KeywordsTRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / cellular response to estrogen stimulus / estrogen response element binding / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / positive regulation of DNA-binding transcription factor activity ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / cellular response to estrogen stimulus / estrogen response element binding / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / positive regulation of DNA-binding transcription factor activity / negative regulation of cell growth / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / PIP3 activates AKT signaling / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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
Chem-I1D / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsFuruya, N. / Handa, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Steroid Biochem.Mol.Biol. / Year: 2022
Title: Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives.
Authors: Handa, C. / Yamazaki, Y. / Yonekubo, S. / Furuya, N. / Momose, T. / Ozawa, T. / Furuishi, T. / Fukuzawa, K. / Yonemochi, E.
History
DepositionMay 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2022Group: Database references / Structure summary / Category: citation / struct / Item: _citation.journal_volume / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor beta
B: Estrogen receptor beta
C: SRC peptide
D: SRC peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7266
Polymers58,1784
Non-polymers5472
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-35 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.728, 88.580, 101.252
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estrogen receptor beta / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 27702.578 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: C334S,C369S,C481S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92731
#2: Protein/peptide SRC peptide


Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-I1D / (2~{R})-3-(2-chloranyl-4-oxidanyl-phenyl)-2-(4-hydroxyphenyl)propanenitrile


Mass: 273.714 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12ClNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.08→46.06 Å / Num. obs: 28068 / % possible obs: 97.5 % / Redundancy: 6.4 % / CC1/2: 0.995 / Net I/σ(I): 5.6
Reflection shellResolution: 2.08→2.13 Å / Num. unique obs: 1689 / CC1/2: 0.068

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2giu

2giu


Resolution: 2.08→46.06 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.903 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1387 5 %RANDOM
Rwork0.241 ---
obs0.2673 28068 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 93.65 Å2 / Biso mean: 36.228 Å2 / Biso min: 22.87 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0 Å20 Å2
2--1.74 Å2-0 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 2.08→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3427 0 38 10 3475
Biso mean--40.91 31.35 -
Num. residues----464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133521
X-RAY DIFFRACTIONr_bond_other_d0.0360.0173327
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.6144752
X-RAY DIFFRACTIONr_angle_other_deg2.3681.577708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9715455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62423.866119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7115630
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.304159
X-RAY DIFFRACTIONr_chiral_restr0.0720.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023820
X-RAY DIFFRACTIONr_gen_planes_other0.010.02643
X-RAY DIFFRACTIONr_mcbond_it3.3543.9721839
X-RAY DIFFRACTIONr_mcbond_other3.3483.971838
X-RAY DIFFRACTIONr_mcangle_it4.8565.9432289
LS refinement shellResolution: 2.08→2.13 Å
RfactorNum. reflection% reflection
Rfree0.689 41 -
Rwork0.67 798 -
obs--30.31 %

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