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- PDB-2giu: Human estrogen receptor beta ligand-binding domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 2giu
TitleHuman estrogen receptor beta ligand-binding domain in complex with compound 45
ComponentsEstrogen receptor beta
KeywordsTRANSCRIPTION REGULATOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ER-BETA / 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-FBR / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT / Resolution: 2.2 Å
AuthorsFitzgerald, P.M.D. / Sharma, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: The discovery of tetrahydrofluorenones as a new class of estrogen receptor beta-subtype selective ligands.
Authors: Wilkening, R.R. / Ratcliffe, R.W. / Tynebor, E.C. / Wildonger, K.J. / Fried, A.K. / Hammond, M.L. / Mosley, R.T. / Fitzgerald, P.M.D. / Sharma, N. / McKeever, B.M. / Nilsson, S. / Carlquist, ...Authors: Wilkening, R.R. / Ratcliffe, R.W. / Tynebor, E.C. / Wildonger, K.J. / Fried, A.K. / Hammond, M.L. / Mosley, R.T. / Fitzgerald, P.M.D. / Sharma, N. / McKeever, B.M. / Nilsson, S. / Carlquist, M. / Thorsell, A. / Locco, L. / Katz, R. / Frisch, K. / Birzin, E.T. / Wilkinson, H.A. / Mitra, S. / Cai, S. / Hayes, E.C. / Schaeffer, J.M. / Rohrer, S.P.
History
DepositionMar 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5582
Polymers27,2221
Non-polymers3351
Water1,06359
1
A: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1154
Polymers54,4452
Non-polymers6702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Unit cell
Length a, b, c (Å)64.530, 64.530, 251.160
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1020-

HOH

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 27222.299 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN (Residues 260-500)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92731
#2: Chemical ChemComp-FBR / (9aS)-4-bromo-9a-butyl-7-hydroxy-1,2,9,9a-tetrahydro-3H-fluoren-3-one


Mass: 335.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19BrO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.77 Å3/Da / Density % sol: 55.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: Precipitant 1.8 M NaCl, 6% PEG 6000, 3% isopropanol, 50 mM Tris buffer pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 12, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.2→99.9 Å / Num. obs: 14390 / % possible obs: 97.3 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 28.51
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.43 / % possible all: 64.3

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Processing

Software
NameClassification
X-GENdata scaling
X-GENdata reduction
SHELXLrefinement
MAR345data collection
RefinementMethod to determine structure: RIGID-BODY REFINEMENT
Starting model: ER-BETA+GENIESTEIN

Resolution: 2.2→8 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.323 702 5 %random
Rwork0.227 ---
obs0.227 13267 97.3 %-
all-13267 --
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1761 0 20 59 1840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.004
X-RAY DIFFRACTIONs_angle_d0.019
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.271
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.028
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.006

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