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- PDB-1l2j: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -

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Basic information

Entry
Database: PDB / ID: 1l2j
TitleHuman Estrogen Receptor beta Ligand-binding Domain in Complex with (R,R)-5,11-cis-diethyl-5,6,11,12-tetrahydrochrysene-2,8-diol
ComponentsESTROGEN RECEPTOR BETA
Keywordstranscription receptor / nuclear receptor / transcription factor / estrogen / antagonist
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 / 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 / chromatin / regulation of DNA-templated transcription / 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-ETC / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsShiau, A.K. / Barstad, D. / Radek, J.T. / Meyers, M.J. / Nettles, K.W. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Agard, D.A. / Greene, G.L.
Citation
Journal: Nat.Struct.Biol. / Year: 2002
Title: Structural characterization of a subtype-selective ligand reveals a novel mode of estrogen receptor antagonism.
Authors: Shiau, A.K. / Barstad, D. / Radek, J.T. / Meyers, M.J. / Nettles, K.W. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A. / Agard, D.A. / Greene, G.L.
#1: 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. / Gustafsson, J.A. / Carlquist, M.
#2: Journal: J.Med.Chem. / Year: 1999
Title: Estrogen Receptor Subtype-selective Ligands: Asymmetric Synthesis and Biological Evaluation of cis- and trans-5,11-dialkyl-5,6,11,12-tetrahydrochrysenes
Authors: Meyers, M.J. / Sun, J. / Carlson, K.E. / Katzenellenbogen, B.S. / Katzenellenbogen, J.A.
History
DepositionFeb 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: ESTROGEN RECEPTOR BETA
B: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7834
Polymers61,1422
Non-polymers6412
Water1629
1
A: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8922
Polymers30,5711
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8922
Polymers30,5711
Non-polymers3201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: ESTROGEN RECEPTOR BETA
hetero molecules

B: ESTROGEN RECEPTOR BETA
hetero molecules

B: ESTROGEN RECEPTOR BETA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,6756
Polymers91,7133
Non-polymers9613
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7520 Å2
ΔGint-62 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.144, 99.144, 193.383
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a homodimer which is not observed in the crystal.

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Components

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


Mass: 30571.119 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (residues 256-505)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92731
#2: Chemical ChemComp-ETC / (R,R)-5,11-CIS-DIETHYL-5,6,11,12-TETRAHYDROCHRYSENE-2,8-DIOL / (R,R)-Tetrahydrochrysene


Mass: 320.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H24O2 / Comment: antagonist*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.99 Å3/Da / Density % sol: 67.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.5-1.75 M Ammonium sulfate, 100 mM Sodium Acetate pH 4.8-5.2 294-296 K, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 21-23 ℃ / PH range low: 5.2 / PH range high: 4.8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14.8 mg/mlprotein1drop
21.5-1.75 Mammonium sulfate1reservoir
3100 mMsodium acetate1reservoirpH4.8-5.2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.07 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 1999
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 2.95→49.6 Å / Num. all: 14895 / Num. obs: 14895 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 46.7 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.3
Reflection shellResolution: 2.95→3.06 Å / Mean I/σ(I) obs: 3.4 / Num. unique all: 1507 / Rsym value: 0.302 / % possible all: 100
Reflection
*PLUS
Num. measured all: 64540 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.302

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1A52, 1ERE, 1ERR, 3ERD, 3ERT

1a52

1ere

1err

3erd

3ert


Resolution: 2.95→49.6 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 10000 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The structure was refined against data which had been sharpened with a -55 A**2 correction factor.
RfactorNum. reflection% reflectionSelection details
Rfree0.299 741 5 %Random
Rwork0.259 ---
all-14893 --
obs-14893 99.6 %-
Solvent computationSolvent model: flat model / Bsol: 33.127 Å2 / ksol: 0.333695 e/Å3
Displacement parametersBiso mean: 40.08 Å2
Baniso -1Baniso -2Baniso -3
1-12.434 Å25.662 Å20 Å2
2--12.434 Å20 Å2
3----24.867 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 2.95→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 48 9 3459
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.29
X-RAY DIFFRACTIONc_dihedral_angle_d17.92
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.7931.5
X-RAY DIFFRACTIONc_mcangle_it3.0712
X-RAY DIFFRACTIONc_scbond_it2.6722
X-RAY DIFFRACTIONc_scangle_it4.1152.5
Refine LS restraints NCSNCS model details: constrained
LS refinement shellResolution: 2.95→3.06 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3509 65 4.3 %
Rwork0.3397 1445 -
obs-1510 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Rfactor obs: 0.259 / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.259
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17.92
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor Rfree: 0.351 / Rfactor Rwork: 0.34 / Rfactor obs: 0.34

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