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- PDB-1qkn: RAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1qkn
TitleRAT OESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH ANTAGONIST RALOXIFENE
ComponentsESTROGEN RECEPTOR BETA
KeywordsNUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ANTAGONIST
Function / homology
Function and homology information


negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to insecticide / estradiol binding / epithelial cell maturation involved in prostate gland development / amygdala development ...negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / response to insecticide / estradiol binding / epithelial cell maturation involved in prostate gland development / amygdala development / response to human chorionic gonadotropin / hormone-mediated apoptotic signaling pathway / Extra-nuclear estrogen signaling / Sertoli cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / prostate gland development / Sertoli cell development / Nuclear Receptor transcription pathway / response to genistein / hormone binding / organic cyclic compound binding / negative regulation of androgen receptor signaling pathway / steroid hormone binding / response to salt / prostate gland epithelium morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / heterocyclic compound binding / nuclear steroid receptor activity / hypothalamus development / negative regulation of feeding behavior / nuclear estrogen receptor activity / female gonad development / response to dexamethasone / vagina development / androgen receptor signaling pathway / response to testosterone / uterus development / cellular response to organic cyclic compound / behavioral fear response / negative regulation of reactive oxygen species metabolic process / estrous cycle / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / ovarian follicle development / estrogen receptor signaling pathway / steroid binding / response to hormone / cerebellum development / response to nutrient levels / epithelial cell proliferation / protein-DNA complex / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / negative regulation of smooth muscle cell proliferation / positive regulation of DNA-binding transcription factor activity / neuron migration / brain development / response to organic cyclic compound / response to estrogen / vasodilation / male gonad development / nuclear receptor activity / negative regulation of epithelial cell proliferation / cellular response to xenobiotic stimulus / response to estradiol / regulation of cell population proliferation / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / perikaryon / response to ethanol / negative regulation of neuron apoptotic process / sequence-specific DNA binding / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / learning or memory / positive regulation of apoptotic process / response to xenobiotic stimulus / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / neuronal cell body / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleus / cytoplasm
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 ...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
ACETATE ION / RALOXIFENE / Estrogen receptor beta
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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)29,2193
Polymers28,6861
Non-polymers5332
Water2,306128
1
A: ESTROGEN RECEPTOR BETA
hetero molecules

A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4376
Polymers57,3722
Non-polymers1,0654
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area3740 Å2
ΔGint-21.4 kcal/mol
Surface area24880 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.550, 67.550, 148.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsBIOLOGICAL_UNIT: DIMER

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Components

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


Mass: 28686.002 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH THE ANTAGONIST RALOXIFENE / Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: OESTROGEN RECEPTOR BETA / Plasmid: PLEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q62986
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-RAL / RALOXIFENE


Mass: 473.583 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H27NO4S / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBINDS ESTROGENS WITH AN AFFINITY SIMILAR TO THAT OF ERALPHA, AND ACTIVATES EXPRESSION OF REPORTER ...BINDS ESTROGENS WITH AN AFFINITY SIMILAR TO THAT OF ERALPHA, AND ACTIVATES EXPRESSION OF REPORTER GENES CONTAINING ESTROGEN RESPONSE ELEMENTS (ERE) IN AN ESTROGEN-DEPENDENT MANNER.

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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: 2.87 Å3/Da / Density % sol: 57 %
Crystal growpH: 4.8
Details: 7.5% (W/V) PEG 4000, 0.1M AMMONIUM ACETATE, 3% (W/V) DIMETHYLFORMAMIDE, 0.025M SODIUM ACETATE, PH 4.8
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Details: drop consists of 1:2 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17-11 mg/mlprotein1drop
27.5 %(w/v)PEG40001reservoir
30.1 Mammonium acetate1reservoir
43 %(v/v)dimethylformamide1reservoir
525 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9096
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 30, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9096 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. obs: 16904 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.077 / Net I/σ(I): 8.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.467 / % possible all: 98.7
Reflection
*PLUS
Num. measured all: 97187 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 98.7 % / Rmerge(I) obs: 0.467

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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: 2.25→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24392 / ESU R Free: 0.22001
Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. THE C-TERMINAL HELIX (H12) IS VISIBLE BUT POORLY DEFINED IN THE ELECTRON DENSITY MAPS. CONSEQUENTLY THIS ...Details: BULK SOLVENT CORRECTION CALCULATED IN XPLOR V3.843 WAS USED THROUGHOUT REFINEMENT. THE C-TERMINAL HELIX (H12) IS VISIBLE BUT POORLY DEFINED IN THE ELECTRON DENSITY MAPS. CONSEQUENTLY THIS REGION HAS EXTREMELY HIGH TEMPERATURE FACTORS BUT ITS INCLUSION IN THE MODEL WAS REFLECTED BY AN APPRECIABLE DROP IN FREE R FACTOR.
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1691 10 %RANDOM
Rwork0.204 ---
obs-16870 99 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-3.592 Å20 Å20 Å2
2--3.592 Å20 Å2
3----6.691 Å2
Refinement stepCycle: LAST / Resolution: 2.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1750 0 38 128 1916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.02
X-RAY DIFFRACTIONp_angle_d0.0380.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1832
X-RAY DIFFRACTIONp_mcangle_it3.433
X-RAY DIFFRACTIONp_scbond_it2.5162
X-RAY DIFFRACTIONp_scangle_it3.7543
X-RAY DIFFRACTIONp_plane_restr0.0120.02
X-RAY DIFFRACTIONp_chiral_restr0.1360.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.3350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1660.3
X-RAY DIFFRACTIONp_planar_tor27
X-RAY DIFFRACTIONp_staggered_tor18.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.920
X-RAY DIFFRACTIONp_special_tor

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