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- PDB-5toa: Crystal Structure of ER beta bound to Estradiol -

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Basic information

Entry
Database: PDB / ID: 5toa
TitleCrystal Structure of ER beta bound to Estradiol
ComponentsEstrogen receptor beta
KeywordsTRANSCRIPTION / Estrogen receptor / estradiol / Helix 12 / 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 / 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
ESTRADIOL / Estrogen receptor beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTextor, L. / Nascimento, A.S. / Polikarpov, I.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/22007-0 Brazil
Sao Paulo Research Foundation (FAPESP)2013/08293-7 Brazil
Sao Paulo Research Foundation (FAPESP)2012/24750-6 Brazil
CitationJournal: Sci Rep / Year: 2017
Title: An alternative conformation of ER beta bound to estradiol reveals H12 in a stable antagonist position.
Authors: Souza, P.C.T. / Textor, L.C. / Melo, D.C. / Nascimento, A.S. / Skaf, M.S. / Polikarpov, I.
History
DepositionOct 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,6034
Polymers56,0582
Non-polymers5452
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-20 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.811, 83.811, 168.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Estrogen receptor beta / / ER-beta / Nuclear receptor subfamily 3 group A member 2


Mass: 28029.234 Da / Num. of mol.: 2 / Fragment: UNP residues 262-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92731
#2: Chemical ChemComp-EST / ESTRADIOL / Estradiol


Mass: 272.382 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H24O2 / Comment: hormone*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Na-citrate, 10% [w/v] PEG-4000, 10% [v/v] isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: Si(111) Silicon Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.5→44.4 Å / Num. obs: 24377 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.9
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2697 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OLL

3oll


Resolution: 2.5→44.425 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2445 1199 4.92 %
Rwork0.2054 --
obs0.2074 24354 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→44.425 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3553 0 40 63 3656
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023672
X-RAY DIFFRACTIONf_angle_d0.5974990
X-RAY DIFFRACTIONf_dihedral_angle_d12.4982254
X-RAY DIFFRACTIONf_chiral_restr0.036609
X-RAY DIFFRACTIONf_plane_restr0.005610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5003-2.60040.35821190.31572522X-RAY DIFFRACTION100
2.6004-2.71870.31771320.28252534X-RAY DIFFRACTION100
2.7187-2.8620.29311280.26762539X-RAY DIFFRACTION100
2.862-3.04130.31051350.24942551X-RAY DIFFRACTION100
3.0413-3.2760.29021340.22812543X-RAY DIFFRACTION100
3.276-3.60560.25361350.21252568X-RAY DIFFRACTION100
3.6056-4.1270.22271360.18542580X-RAY DIFFRACTION100
4.127-5.19830.20541370.16742610X-RAY DIFFRACTION100
5.1983-44.43220.22311430.19052708X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05560.04090.03850.06640.01760.06480.04660.4016-1.43330.4923-0.6188-0.50380.6743-0.1683-0.00050.6873-0.20750.03270.65180.09291.2325.226415.14575.8191
20.5066-0.51370.08960.3595-0.06020.78010.6290.4228-0.17090.3119-0.5561-0.31840.1174-0.4759-0.00080.4889-0.0357-0.01650.68290.04370.59078.569425.40493.3353
30.15410.3389-0.09941.79610.62930.73260.8585-0.4198-0.0339-0.1191-0.0856-1.5603-0.70910.94690.03790.8474-0.14870.07770.4438-0.0110.606715.78642.87981.6313
43.7592-1.3527-3.24321.96281.47362.8664-0.04480.83550.4439-0.6853-0.95521.68190.1011-1.5722-0.06921.438-0.5799-0.05350.62150.05780.961726.207154.88856.9608
52.7895-0.2436-0.08621.52380.06062.11490.0579-0.05340.07030.2006-0.02630.0559-0.1196-0.092-0.00010.4714-0.0106-0.00790.43160.00090.487312.665337.724912.7421
61.8765-0.2495-0.02352.28341.10032.63870.0919-0.3145-0.01330.0278-0.1085-0.4183-0.07430.2232-0.00010.469-0.0544-0.06030.50580.0370.512223.990734.489413.2727
70.3835-0.0399-0.92660.0456-0.01872.5183-0.55760.2018-0.6162-0.1710.911.42542.4634-1.3755-0.11820.7163-0.0516-0.14810.73470.16641.0354-0.069626.356324.8684
80.79680.20541.00331.27330.07320.7792-0.14760.081-1.2857-0.2432-0.18441.08530.10840.0296-0.00060.6074-0.0862-0.05670.46890.03320.673910.234816.735313.3715
91.70531.0449-0.06451.05220.01833.2229-0.1804-0.22270.00370.73080.30860.19740.00080.19460.00010.5793-0.0091-0.08770.5864-0.02230.513620.695932.589721.0154
100.80740.8045-0.74662.5572-0.4020.6855-0.17280.15870.7063-0.3479-0.08940.3298-0.2609-0.238-0.00030.71390.08080.1040.550.05650.77973.911447.429114.1659
111.43730.85681.45290.4350.71241.7237-0.7280.3292-2.03690.8230.9145-1.10561.49012.04170.08091.2312-0.2105-0.3540.79470.20640.874330.31396.851933.4756
120.22290.20820.30410.0890.22680.2588-0.4277-0.4986-0.50491.2091-0.23410.91640.3349-0.5861-0.00080.97040.0003-0.09310.86280.18890.641625.965816.236745.5799
130.275-0.44090.15760.7743-0.24010.1115-0.0977-0.10720.35340.3541-0.4562-0.3057-0.47960.1286-0.01371.20220.00750.21521.6755-0.0180.615412.80434.201157.3215
142.81610.90871.04342.64280.27092.60730.0013-0.5205-0.13270.23830.11820.02680.2614-0.213800.5878-0.0318-0.04970.71120.06250.517625.212527.18840.8161
150.06010.28860.48950.59210.90980.9330.3158-1.12070.53050.6341-0.3020.1316-0.1429-1.2185-0.00070.70730.05840.11651.27490.02720.78759.602732.315247.9153
160.88080.55441.01441.08510.04751.70880.0416-0.4659-0.13620.140.18820.23420.3528-0.963800.5985-0.0914-0.06090.87370.17120.690713.506422.014135.4118
174.7663-2.8052-3.87621.57682.19013.61760.45440.96322.0599-2.4905-0.78280.9138-3.29710.4051-0.08531.4282-0.254-0.18170.73870.13561.002829.450927.080627.3997
180.476-0.80770.15053.2189-0.12073.68850.0543-0.3036-0.465-0.03160.28530.11130.7576-0.08950.00080.8057-0.1076-0.15990.47250.05770.756920.946714.100225.4633
191.2039-0.26760.72690.6154-0.52790.66340.0279-0.49690.44080.49370.2278-0.4045-0.48-0.38810.00010.78220.0572-0.08860.8624-0.08690.699120.102741.192438.4311
200.1688-0.0114-0.09550.31790.42280.3445-0.2518-0.3738-0.16440.82070.0072-0.4878-0.0305-0.11480.00190.6119-0.0736-0.0390.6190.00650.633934.571534.361746.1005
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 262:266)
2X-RAY DIFFRACTION2(chain A and resid 267:277)
3X-RAY DIFFRACTION3(chain A and resid 278:282)
4X-RAY DIFFRACTION4(chain A and resid 283:290)
5X-RAY DIFFRACTION5(chain A and resid 291:355)
6X-RAY DIFFRACTION6(chain A and resid 356:408)
7X-RAY DIFFRACTION7(chain A and resid 409:424)
8X-RAY DIFFRACTION8(chain A and resid 425:444)
9X-RAY DIFFRACTION9(chain A and resid 445:487)
10X-RAY DIFFRACTION10(chain A and resid 488:501)
11X-RAY DIFFRACTION11(chain B and resid 262:270)
12X-RAY DIFFRACTION12(chain B and resid 271:281)
13X-RAY DIFFRACTION13(chain B and resid 282:289)
14X-RAY DIFFRACTION14(chain B and resid 290:353)
15X-RAY DIFFRACTION15(chain B and resid 354:372)
16X-RAY DIFFRACTION16(chain B and resid 373:404)
17X-RAY DIFFRACTION17(chain B and resid 405:411)
18X-RAY DIFFRACTION18(chain B and resid 422:465)
19X-RAY DIFFRACTION19(chain B and resid 466:488)
20X-RAY DIFFRACTION20(chain B and resid 489:501)

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