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- PDB-2fsz: A second binding site for hydroxytamoxifen within the coactivator... -

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Basic information

Entry
Database: PDB / ID: 2fsz
TitleA second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta
ComponentsEstrogen receptor beta
KeywordsHORMONE/GROWTH FACTOR / nuclear hormone binding domain / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / 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 / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Estrogen receptor beta-like, N-terminal / Estrogen receptor beta/gamma / Estrogen receptor beta / Estrogen receptor/oestrogen-related receptor / Retinoid X Receptor / Retinoid X 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-HYDROXYTAMOXIFEN / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWang, Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: A second binding site for hydroxytamoxifen within the coactivator-binding groove of estrogen receptor beta
Authors: Wang, Y. / Chirgadze, N.Y. / Briggs, S.L. / Khan, S. / Jensen, E.V. / Burris, T.P.
History
DepositionJan 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)57,0386
Polymers55,4882
Non-polymers1,5504
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-24 kcal/mol
Surface area23590 Å2
MethodPISA
2
A: Estrogen receptor beta
B: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
B: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
B: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
B: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,15024
Polymers221,9508
Non-polymers6,20016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
Buried area28930 Å2
ΔGint-156 kcal/mol
Surface area79410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.040, 105.040, 102.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 27743.779 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 / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q92731
#2: Chemical
ChemComp-OHT / 4-HYDROXYTAMOXIFEN


Mass: 387.514 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H29NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1M sodium citrate, 1.5M sodium chloride, 4% ethylene imine, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 28566 / Num. obs: 27338 / % possible obs: 95.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3 / Biso Wilson estimate: 31.9 Å2
Reflection shellResolution: 2.19→2.27 Å / % possible all: 67.4

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
CNX2002refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.11 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2226156.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1019 3.7 %RANDOM
Rwork0.273 ---
all0.274 28181 --
obs0.274 27270 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.776 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 40.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.97 Å20 Å20 Å2
2--5.97 Å20 Å2
3----11.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3561 0 116 40 3717
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.372
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it2.932.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 142 3.8 %
Rwork0.335 3644 -
obs-3628 81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2oht.topoht.par
X-RAY DIFFRACTION3water.topwater_rep.param

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