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- PDB-1qkm: HUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 1qkm
TitleHUMAN OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH PARTIAL AGONIST GENISTEIN
ComponentsESTROGEN RECEPTOR BETA
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / PHYTO-OESTROGEN / PARTIAL 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
GENISTEIN / Estrogen receptor beta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPike, A.C.W. / Brzozowski, A.M. / Carlquist, M.
Citation
Journal: Embo J. / Year: 1999
Title: Structure of the Ligand-Binding Domain of Oestrogen Receptor Beta in the Presence of a Partial Agonist and a Full Antagonist
Authors: Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M.
#1: Journal: Nature / Year: 1997
Title: Molecular Basis of Agonism and Antagonism in the Oestrogen Receptor
Authors: Brzozowski, A.M. / Pike, A.C.W. / Dauter, Z. / Hubbard, R.E. / Bonn, T. / Engstrom, O. / Ohman, L. / Greene, G.L. / Gustaffson, J.-A. / Carlquist, M.
History
DepositionJul 27, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9962
Polymers28,7261
Non-polymers2701
Water2,504139
1
A: ESTROGEN RECEPTOR BETA
hetero molecules

A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9934
Polymers57,4522
Non-polymers5402
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area3760 Å2
ΔGint-30.4 kcal/mol
Surface area24810 Å2
MethodPQS
Unit cell
Length a, b, c (Å)63.120, 63.120, 250.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBIOLOGICAL_UNIT: DIMER

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Components

#1: Protein ESTROGEN RECEPTOR BETA / / OESTROGEN RECEPTOR / ER-LBD


Mass: 28726.092 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH THE PHYTO-OESTROGEN GENISTEIN / Source: (gene. exp.) HOMO SAPIENS (human) / Gene: OESTROGEN RECEPTOR BETA / Plasmid: PLEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q92731
#2: Chemical ChemComp-GEN / GENISTEIN / 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE / 4',5,7-TRIHYDROXYISOFLAVONE / PRUNETOL / GENISTEOL / Genistein


Mass: 270.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H10O5 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.44 Å3/Da / Density % sol: 49 %
Crystal growpH: 8.1
Details: 6-9% (W/V) PEG 6000, 1.6-2.1M NACL, 0.1M TRIS-HCL, PH 8.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
26-9 %(w/v)PEG60001reservoir
31.6-2.1 M1reservoirNaCl
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 1.8→60 Å / Num. obs: 28523 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 32.6 Å2 / Rsym value: 0.049 / Net I/σ(I): 15
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 8 % / Mean I/σ(I) obs: 4 / Rsym value: 0.433 / % possible all: 100
Reflection
*PLUS
Num. measured all: 358818 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.433

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERE

1ere


Resolution: 1.8→55 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12715 / ESU R Free: 0.12556
Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT. DISCREPANCY BETWEEN REFINEMENT STATISTICS GIVEN ABOVE AND PUBLISHED VALUES ARISE DUE TO A SEQUENCE ERROR THAT HAS SUBSEQUENTLY BEEN CORRECTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1441 5 %RANDOM
Rwork0.215 ---
obs-28460 99.7 %-
Displacement parametersBiso mean: 41.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.115 Å2-1.138 Å20 Å2
2--3.116 Å20 Å2
3----3.827 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 20 139 1940
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.8512
X-RAY DIFFRACTIONp_mcangle_it2.8473
X-RAY DIFFRACTIONp_scbond_it2.3592
X-RAY DIFFRACTIONp_scangle_it3.7453
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd0.1810.3
X-RAY DIFFRACTIONp_multtor_nbd0.3610.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1160.3
X-RAY DIFFRACTIONp_planar_tor2.67
X-RAY DIFFRACTIONp_staggered_tor16.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.720
X-RAY DIFFRACTIONp_special_tor

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