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- PDB-1nde: Estrogen Receptor beta with Selective Triazine Modulator -

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Basic information

Entry
Database: PDB / ID: 1nde
TitleEstrogen Receptor beta with Selective Triazine Modulator
ComponentsEstrogen receptor beta
KeywordsTRANSCRIPTION / estrogen receptor / estrogen receptor beta / ER / ERb / triazine / estrogen / estradiol / oestrogen
Function / homology
Function and homology information


receptor antagonist activity / nuclear estrogen receptor activity / nuclear steroid receptor activity / estrogen response element binding / positive regulation of DNA-binding transcription factor activity / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth ...receptor antagonist activity / nuclear estrogen receptor activity / nuclear steroid receptor activity / estrogen response element binding / positive regulation of DNA-binding transcription factor activity / estrogen receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / Nuclear Receptor transcription pathway / nuclear receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell signaling / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / Extra-nuclear estrogen signaling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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 ...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 / Double treble clef zinc finger, C4 type / 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-MON / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHenke, B.R. / Consler, T.G. / Go, N. / Hale, R.L. / Hohman, D.R. / Jones, S.A. / Lu, A.T. / Moore, L.B. / Moore, J.T. / Orband-Miller, L.A. ...Henke, B.R. / Consler, T.G. / Go, N. / Hale, R.L. / Hohman, D.R. / Jones, S.A. / Lu, A.T. / Moore, L.B. / Moore, J.T. / Orband-Miller, L.A. / Robinett, R.G. / Shearin, J. / Spearing, P.K. / Stewart, E.L. / Turnbull, P.S. / Weaver, S.L. / Williams, S.P. / Wisely, G.B. / Lambert, M.H.
CitationJournal: J.Med.Chem. / Year: 2002
Title: A New Series of Estrogen Receptor Modulators That Display Selectivity for Estrogen Receptor beta
Authors: Henke, B.R. / Consler, T.G. / Go, N. / Hale, R.L. / Hohman, D.R. / Jones, S.A. / Lu, A.T. / Moore, L.B. / Moore, J.T. / Orband-Miller, L.A. / Robinett, R.G. / Shearin, J. / Spearing, P.K. / ...Authors: Henke, B.R. / Consler, T.G. / Go, N. / Hale, R.L. / Hohman, D.R. / Jones, S.A. / Lu, A.T. / Moore, L.B. / Moore, J.T. / Orband-Miller, L.A. / Robinett, R.G. / Shearin, J. / Spearing, P.K. / Stewart, E.L. / Turnbull, P.S. / Weaver, S.L. / Williams, S.P. / Wisely, G.B. / Lambert, M.H.
History
DepositionDec 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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)29,5962
Polymers29,1111
Non-polymers4851
Water77543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1914
Polymers58,2212
Non-polymers9702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x-y,-y,-z-11
Buried area4960 Å2
ΔGint-39 kcal/mol
Surface area21160 Å2
MethodPISA, PQS
3
A: Estrogen receptor beta
hetero molecules

A: Estrogen receptor beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1914
Polymers58,2212
Non-polymers9702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-5/61
Buried area4260 Å2
ΔGint-31 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.558, 65.558, 239.30
Angle α, β, γ (deg.)90, 90, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Estrogen receptor beta / ER-beta


Mass: 29110.553 Da / Num. of mol.: 1 / Fragment: residues 256-501
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESTRB / Plasmid: pERb256-501 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21[DE3] / References: UniProt: Q92731
#2: Chemical ChemComp-MON / 4-(2-{[4-{[3-(4-CHLOROPHENYL)PROPYL]SULFANYL}-6-(1-PIPERAZINYL)-1,3,5-TRIAZIN-2-YL]AMINO}ETHYL)PHENOL


Mass: 485.045 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H29ClN6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50mM PIPES pH6.5, 200 mM lithium sulfate, 8-12% PEG35000, 5% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 22K, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMPIPES1droppH6.5
2200 mMlithium sulfate1drop
38-12 %PEG350001drop
45 %sucrose1drop
55 %glycerol1reservoir
620 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 6816 / Num. obs: 6686 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 20 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 3.1
Reflection shellResolution: 3→3.11 Å / Redundancy: 20 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.1 / Num. unique all: 635 / Rsym value: 0.4 / % possible all: 100
Reflection
*PLUS
Num. obs: 6757 / Num. measured all: 120828 / Rmerge(I) obs: 0.09
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.4

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Processing

Software
NameClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ERR

1err


Resolution: 3→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used Maximum Likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.273 355 -Random
Rwork0.24 ---
obs0.24 6382 95.6 %-
all-6674 --
Displacement parametersBiso mean: 65.16 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1788 0 33 43 1864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.00928
X-RAY DIFFRACTIONx_angle_deg2.0132
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.296 40 -
Rwork0.315 --
obs-687 0.98 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 7 % / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.0093
X-RAY DIFFRACTIONx_angle_deg2.01

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