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- PDB-5w9d: Estrogen Receptor Alpha Ligand Binding Domain C381S, C417S, C530S... -

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Basic information

Entry
Database: PDB / ID: 5w9d
TitleEstrogen Receptor Alpha Ligand Binding Domain C381S, C417S, C530S Mutant in Complex with Endoxifen
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Selective Estrogen Receptor Modulator
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / 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 development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / regulation of branching involved in prostate gland morphogenesis / 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 development / steroid hormone receptor signaling pathway / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / mammary gland alveolus development / cellular response to estrogen stimulus / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of DNA-binding transcription factor activity / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of nitric-oxide synthase activity / estrogen receptor signaling pathway / protein localization to chromatin / steroid binding / 14-3-3 protein binding / negative regulation of canonical NF-kappaB signal transduction / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of miRNA transcription / ESR-mediated signaling / TBP-class protein binding / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription coregulator binding / transcription corepressor binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / male gonad development / nuclear receptor activity / Ovarian tumor domain proteases / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / positive regulation of cytosolic calcium ion concentration / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / DNA-binding transcription activator activity, RNA polymerase II-specific / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / calmodulin binding / Extra-nuclear estrogen signaling / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / protein kinase binding / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / 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 / 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
Endoxifen / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6464 Å
AuthorsFanning, S.W. / Greene, G.L.
CitationJournal: Mol. Pharmacol. / Year: 2018
Title: Endoxifen, 4-Hydroxytamoxifen and an Estrogenic Derivative Modulate Estrogen Receptor Complex Mediated Apoptosis in Breast Cancer.
Authors: Maximov, P.Y. / Abderrahman, B. / Fanning, S.W. / Sengupta, S. / Fan, P. / Curpan, R.F. / Rincon, D.M.Q. / Greenland, J.A. / Rajan, S.S. / Greene, G.L. / Jordan, V.C.
History
DepositionJun 23, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 4, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

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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)57,4574
Polymers56,7102
Non-polymers7472
Water11,079615
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-16 kcal/mol
Surface area20780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.980, 57.980, 277.001
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 28355.207 Da / Num. of mol.: 2
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-9XY / Endoxifen / 4-[(1Z)-1-{4-[2-(methylamino)ethoxy]phenyl}-2-phenylbut-1-en-1-yl]phenol


Mass: 373.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H27NO2 / Comment: inhibitor*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8,000, Magnesium Chloride, Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.646→19.615 Å / Num. obs: 56989 / % possible obs: 90.03 % / Redundancy: 3.7 % / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACC

5acc


Resolution: 1.6464→19.615 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 2850 5 %
Rwork0.1675 --
obs0.169 56989 90.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6464→19.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3779 0 56 615 4450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0184095
X-RAY DIFFRACTIONf_angle_d1.7575564
X-RAY DIFFRACTIONf_dihedral_angle_d14.2961524
X-RAY DIFFRACTIONf_chiral_restr0.096652
X-RAY DIFFRACTIONf_plane_restr0.011697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6464-1.67480.28361200.23092419X-RAY DIFFRACTION81
1.6748-1.70520.26311530.20842586X-RAY DIFFRACTION85
1.7052-1.7380.26171070.19552605X-RAY DIFFRACTION88
1.738-1.77340.20911330.19072644X-RAY DIFFRACTION88
1.7734-1.8120.22551430.18072695X-RAY DIFFRACTION88
1.812-1.85410.19851450.18172651X-RAY DIFFRACTION89
1.8541-1.90040.24281490.1752668X-RAY DIFFRACTION89
1.9004-1.95180.19841490.17652696X-RAY DIFFRACTION90
1.9518-2.00910.19961370.1722690X-RAY DIFFRACTION89
2.0091-2.07390.22561560.17152752X-RAY DIFFRACTION91
2.0739-2.1480.20311240.15422764X-RAY DIFFRACTION92
2.148-2.23390.2051770.15972753X-RAY DIFFRACTION92
2.2339-2.33540.16241490.15892796X-RAY DIFFRACTION94
2.3354-2.45830.20371760.16092776X-RAY DIFFRACTION94
2.4583-2.6120.15891320.1612818X-RAY DIFFRACTION93
2.612-2.81310.19791580.16392789X-RAY DIFFRACTION94
2.8131-3.09520.181340.15922836X-RAY DIFFRACTION93
3.0952-3.54080.19511390.15872806X-RAY DIFFRACTION93
3.5408-4.45240.14081470.14742728X-RAY DIFFRACTION90
4.4524-19.61610.23461220.18682667X-RAY DIFFRACTION88
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)
17.59450.95181.4791.87090.31332.2672-0.20190.091-0.3658-0.03930.04710.0210.25550.21630.10580.15230.02780.06060.089-0.00430.15948.568312.4413-18.7879
22.069-0.5264-0.03811.35740.02092.1271-0.0707-0.1623-0.09170.18890.0459-0.09070.07580.08620.01940.08560.0221-0.00160.0860.01110.097611.231423.0439-15.3642
32.11240.2403-0.29431.26750.13313.2211-0.00620.2016-0.1175-0.1431-0.050.09190.01360.01430.00940.0745-0.00990.00460.0704-0.04140.1157-4.4422.3835-25.8811
41.0164-0.02390.58531.20320.16430.98930.00450.52390.0065-0.06210.0622-0.09850.08070.1612-0.04020.08370.01880.01380.1653-0.03320.07317.753627.4329-21.8029
54.07972.5951-0.52294.5407-0.47642.2418-0.0182-0.01410.4146-0.1007-0.04640.3792-0.35640.00430.07080.14210.0426-0.04420.1327-0.04370.1664-11.675753.041-20.3746
61.15060.14190.09682.1848-0.05991.99990.01980.13290.138-0.2029-0.05840.0343-0.1219-0.0160.01820.11710.01350.00250.07310.00790.088-3.55948.3131-21.3328
72.21410.34720.40082.7025-0.20956.5861-0.022-0.12640.01350.1162-0.0136-0.0140.01470.2218-0.02310.052-0.0030.01780.053-0.02010.1092-8.614537.9823-14.0139
81.75370.56631.22081.9540.69362.9742-0.0093-0.1119-0.12250.51370.01650.3297-0.0118-0.2222-0.04160.0407-0.02230.08520.134-0.02650.1683-15.131232.5927-9.5188
97.46135.51221.16235.75441.13140.977-0.06260.1183-0.0123-0.10090.02070.035-0.0055-0.02760.020.05940.02740.010.0585-0.00440.0444-2.610136.1603-21.7953
102.3541-0.4233-2.45521.8286-0.44653.46790.2817-0.69980.27110.9106-0.1698-0.2502-0.17520.3408-0.180.4325-0.15690.08740.3182-0.10580.15453.645754.0667-6.8672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 306 through 340 )
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 437 )
3X-RAY DIFFRACTION3chain 'A' and (resid 438 through 496 )
4X-RAY DIFFRACTION4chain 'A' and (resid 497 through 549 )
5X-RAY DIFFRACTION5chain 'B' and (resid 307 through 341 )
6X-RAY DIFFRACTION6chain 'B' and (resid 342 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 438 through 465 )
8X-RAY DIFFRACTION8chain 'B' and (resid 466 through 496 )
9X-RAY DIFFRACTION9chain 'B' and (resid 497 through 528 )
10X-RAY DIFFRACTION10chain 'B' and (resid 529 through 545 )

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