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- PDB-1u9e: CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397 -

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Basic information

Entry
Database: PDB / ID: 1u9e
TitleCRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-397
Components
  • Estrogen receptor beta
  • STEROID RECEPTOR COACTIVATOR-1Nuclear receptor coactivator 1
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 / intracellular 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 / intracellular 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 / Nuclear Receptor transcription pathway / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / positive regulation of DNA-binding transcription factor activity / cell-cell signaling / PIP3 activates AKT 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 / chromatin / regulation of DNA-templated transcription / 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 / 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
2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsManas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. ...Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C.
CitationJournal: J.Am.Chem.Soc. / Year: 2004
Title: Structure-Based Design Of Estrogen Receptor-beta Selective Ligands
Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. ...Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C.
History
DepositionAug 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: 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: STEROID RECEPTOR COACTIVATOR-1
D: STEROID RECEPTOR COACTIVATOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0206
Polymers56,5674
Non-polymers4522
Water1,928107
1
A: Estrogen receptor beta
C: STEROID RECEPTOR COACTIVATOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5103
Polymers28,2842
Non-polymers2261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-13 kcal/mol
Surface area11180 Å2
MethodPISA
2
B: Estrogen receptor beta
D: STEROID RECEPTOR COACTIVATOR-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5103
Polymers28,2842
Non-polymers2261
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-16 kcal/mol
Surface area11160 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-45 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.113, 87.935, 99.524
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Estrogen receptor beta / / ER-beta


Mass: 27266.336 Da / Num. of mol.: 2
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: Protein/peptide STEROID RECEPTOR COACTIVATOR-1 / Nuclear receptor coactivator 1


Mass: 1017.239 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: This sequence of this peptide can be found naturally in homo Sapiens (Human).
#3: Chemical ChemComp-397 / 2-(4-HYDROXY-PHENYL)BENZOFURAN-5-OL


Mass: 226.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.66 Å3/Da / Density % sol: 0.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG3350, Mg formate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2000
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. all: 18744 / Num. obs: 18331 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 31
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 6.2 / Num. unique all: 917 / Rsym value: 0.374 / % possible all: 0.995

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: complex structure of ER-beta with genestein.

Resolution: 2.4→19.85 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2516610.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 893 4.9 %RANDOM
Rwork0.231 ---
all0.234 18477 --
obs0.234 18331 99.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.5421 Å2 / ksol: 0.341738 e/Å3
Displacement parametersBiso mean: 30.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.01 Å20 Å20 Å2
2--5.79 Å20 Å2
3----2.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 34 107 3848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.861.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.22
X-RAY DIFFRACTIONc_scangle_it1.862.5
LS refinement shellResolution: 2.4→2.55 Å / Total num. of bins used: 6
RfactorNum. reflection
Rfree0.297 139
Rwork0.264 -
obs-3011
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4397.PAR397.TOP

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