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- PDB-6psj: Bazedoxifene in Complex with Y537S Estrogen Receptor Alpha Ligand... -

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Basic information

Entry
Database: PDB / ID: 6psj
TitleBazedoxifene in Complex with Y537S Estrogen Receptor Alpha Ligand Binding Domain
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen Receptor / Y537S / Bazedoxifene / Steroid / Hormone
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / calmodulin binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / positive regulation of DNA-templated transcription / Golgi apparatus / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / 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
Bazedoxifene / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFanning, S.W. / Greene, G.L.
CitationJournal: Elife / Year: 2022
Title: Stereospecific lasofoxifene derivatives reveal the interplay between estrogen receptor alpha stability and antagonistic activity in ESR1 mutant breast cancer cells.
Authors: Hosfield, D.J. / Weber, S. / Li, N.S. / Suavage, M. / Joiner, C.F. / Hancock, G.R. / Sullivan, E.A. / Ndukwe, E. / Han, R. / Cush, S. / Laine, M. / Mader, S.C. / Greene, G.L. / Fanning, S.W.
History
DepositionJul 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Estrogen receptor
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0094
Polymers60,0682
Non-polymers9412
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-11 kcal/mol
Surface area19430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.195, 56.491, 87.627
Angle α, β, γ (deg.)90.00, 104.32, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Estrogen receptor / ER / ER-alpha / Estradiol receptor / Nuclear receptor subfamily 3 group A member 1


Mass: 30034.029 Da / Num. of mol.: 2 / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-29S / Bazedoxifene / 1-{4-[2-(azepan-1-yl)ethoxy]benzyl}-2-(4-hydroxyphenyl)-3-methyl-1H-indol-5-ol


Mass: 470.603 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H34N2O3 / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.06 Å3/Da / Density % sol: 40.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 8000, magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 43172 / % possible obs: 95 % / Redundancy: 3.6 % / Rpim(I) all: 0.087 / Net I/σ(I): 18.76
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 9.06 / Num. unique obs: 1889 / CC1/2: 0.609 / Rpim(I) all: 0.495 / % possible all: 82.8

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W9D

5w9d


Resolution: 1.8→29.14 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2146 --
Rwork0.1851 --
obs-37382 82.1 %
Refinement stepCycle: LAST / Resolution: 1.8→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3486 0 70 360 3916
LS refinement shellResolution: 1.8→1.83 Å
RfactorNum. reflection
Rfree0.3142 -
Rwork0.2388 -
obs-2042
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)
18.24795.9749-2.75585.5227-3.49024.6116-0.00360.5090.46620.26140.17360.2906-0.6347-0.2548-0.19080.24750.1076-0.00520.1036-0.01890.20691.8858-8.254120.7698
28.25196.7534-5.14338.2908-5.54766.18180.15830.2726-0.0212-0.0482-0.19670.2033-0.0071-0.20090.03160.11330.07810.01580.1616-0.04080.1199-5.7558-21.29320.29
31.73040.8602-1.17452.0418-1.757.5749-0.13530.27480.0329-0.04720.1738-0.04430.003-0.2054-0.04110.03830.0272-0.00530.12420.01060.11264.5799-20.063115.3132
49.4049-0.15187.71793.05560.92497.95090.0845-0.23530.54790.50650.12290.0802-0.6304-0.728-0.14660.2560.07310.0580.1240.00490.1543-2.4148-19.959636.534
57.9147-4.38-1.02212.06952.34478.0131-0.1817-0.926-0.89861.12950.16530.05351.28430.21750.06260.4322-0.0264-0.02180.33160.12230.3435-3.6817-32.537836.8813
62.36481.0184-0.83752.4318-2.16376.4443-0.1051-0.1305-0.07390.17320.0299-0.13410.25840.50080.13360.11380.0786-0.01670.11140.00520.14239.7943-20.179825.2687
72.74191.45772.61185.25435.39518.7429-0.10190.17640.2257-0.00960.2067-0.296-0.39430.1833-0.09630.1649-0.0316-0.03080.10380.05280.197116.7757-10.358915.2378
85.36654.63952.32778.28921.84163.5459-0.0482-0.1481-0.2638-0.0095-0.0334-0.2371-0.04730.16660.06270.11770.09810.00840.1639-0.0010.119713.7772-23.078826.82
92.1865-1.55090.62051.264-1.85346.67960.4830.2832-0.7672-0.17460.06131.20920.6051-1.0061-0.61280.3212-0.1685-0.0430.88380.01970.3719-5.6227-25.12498.4284
101.98210.36010.13199.26212.6983.65910.0918-0.04160.20370.74230.1224-1.0619-0.18530.4065-0.23010.1965-0.0541-0.07930.2945-0.02280.374239.6777-21.249331.3422
112.43850.23530.40355.96542.40723.7457-0.0883-0.3031-0.357-0.12140.0352-0.47860.29080.0624-0.03460.1570.07170.04630.20540.05210.290136.8372-42.390118.0138
122.16780.3622-0.30325.72394.91327.5995-0.2679-0.1944-0.23350.1350.0740.01140.10730.16170.18340.13330.08050.01690.18460.03360.182231.6816-42.048324.3453
132.9939-0.20990.20212.65850.11363.6699-0.0489-0.338-0.02440.41040.01880.05150.01140.02910.00680.190.08570.00490.15810.03230.147627.0259-33.482530.0802
145.213-0.4736-0.63054.76480.32712.310.16091.0485-0.0067-0.762-0.13490.28750.14310.002-0.02820.30680.14270.01360.3966-0.00230.167827.2625-39.90647.7046
156.84696.11951.40727.71482.44523.4938-0.27850.50040.1255-0.84470.2063-0.0053-0.19520.05890.07190.21810.09250.00750.33580.03610.142822.8294-30.05419.9321
162.9279-0.62670.34446.8892-1.30753.8268-0.1715-0.05650.35750.2638-0.0495-0.4279-0.09080.51940.14060.0915-0.0148-0.08530.24870.01890.236629.587-19.956826.8002
176.05744.94550.72762.57130.72851.5147-0.01580.0114-0.1156-0.1824-0.1476-0.13510.00930.14040.16990.09310.06390.00350.17670.01790.118120.3749-25.040719.8234
180.9434-0.6192-0.35281.7288-0.32640.3813-0.0890.3469-0.1472-0.08540.2724-0.1176-0.4316-0.2727-0.07111.0898-0.21780.23270.7633-0.07640.55116.6435-49.598830.0728
199.32566.16471.97756.01165.11787.82850.6468-0.8278-0.78940.6898-0.4623-0.6255-0.0373-0.2372-0.24230.650.05610.03660.33870.0830.186428.8172-44.214736.8368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 341 )
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 363 )
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 394 )
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 407 )
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 421 )
6X-RAY DIFFRACTION6chain 'A' and (resid 422 through 465 )
7X-RAY DIFFRACTION7chain 'A' and (resid 466 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 527 )
9X-RAY DIFFRACTION9chain 'A' and (resid 528 through 550 )
10X-RAY DIFFRACTION10chain 'B' and (resid 307 through 322 )
11X-RAY DIFFRACTION11chain 'B' and (resid 323 through 341 )
12X-RAY DIFFRACTION12chain 'B' and (resid 342 through 363 )
13X-RAY DIFFRACTION13chain 'B' and (resid 364 through 394 )
14X-RAY DIFFRACTION14chain 'B' and (resid 395 through 421 )
15X-RAY DIFFRACTION15chain 'B' and (resid 422 through 437 )
16X-RAY DIFFRACTION16chain 'B' and (resid 438 through 496 )
17X-RAY DIFFRACTION17chain 'B' and (resid 497 through 526 )
18X-RAY DIFFRACTION18chain 'B' and (resid 527 through 535 )
19X-RAY DIFFRACTION19chain 'B' and (resid 536 through 545 )

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