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- PDB-1u3q: Crystal Structure of Estrogen Receptor beta complexed with CL-272 -

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Basic information

Entry
Database: PDB / ID: 1u3q
TitleCrystal Structure of Estrogen Receptor beta complexed with CL-272
ComponentsEstrogen receptor beta
KeywordsTRANSCRIPTION / Estrogen Receptor / Estrogen Receptor Beta / ER-beta / ER / Estrogen / Nuclear Receptor / Transcription Factor / Agonist
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
Chem-272 / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMalamas, M.S. / Manas, E.S. / McDevitt, R.E. / Gunawan, I. / Xu, Z.B. / Collini, M.D. / Miller, C.P. / Dinh, T. / Henderson, R.A. / Keith Jr., J.C. / Harris, H.A.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Design and synthesis of aryl diphenolic azoles as potent and selective estrogen receptor-beta ligands.
Authors: Malamas, M.S. / Manas, E.S. / McDevitt, R.E. / Gunawan, I. / Xu, Z.B. / Collini, M.D. / Miller, C.P. / Dinh, T. / Henderson, R.A. / Keith Jr., J.C. / Harris, H.A.
History
DepositionJul 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Estrogen receptor beta
D: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,4098
Polymers108,4374
Non-polymers9734
Water4,107228
1
A: Estrogen receptor beta
C: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7054
Polymers54,2182
Non-polymers4862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-31 kcal/mol
Surface area19630 Å2
MethodPISA
2
B: Estrogen receptor beta
D: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7054
Polymers54,2182
Non-polymers4862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-30 kcal/mol
Surface area19900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.167, 76.646, 82.800
Angle α, β, γ (deg.)90.00, 111.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Estrogen receptor beta / ER-beta


Mass: 27109.143 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, NR3A2, ESTRB / Plasmid: pET16b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q92731
#2: Chemical
ChemComp-272 / 4-(6-HYDROXY-BENZO[D]ISOXAZOL-3-YL)BENZENE-1,3-DIOL


Mass: 243.215 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.1 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG2000, MgCl, hexaminecobalt trichloride, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Type: ALS / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 35234 / Redundancy: 3.44 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14.95 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 1728 RANDOM
Rwork0.227 --
all0.242 34927 -
obs0.242 34927 -
Refinement stepCycle: LAST / Resolution: 2.4→14.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7153 0 72 228 7453

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