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- PDB-6v8t: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 6v8t
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with LSZ102
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast cancer / acquired drug resistance / hormone therapy / selective estrogen receptor degrader/downregulator
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 / uterus development / negative regulation of smooth muscle cell apoptotic process / 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 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / negative regulation of canonical NF-kappaB signal transduction / ESR-mediated signaling / TBP-class protein binding / negative regulation of miRNA transcription / nitric-oxide synthase regulator activity / nuclear estrogen receptor binding / transcription corepressor binding / transcription coregulator binding / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / transcription coactivator binding / male gonad development / nuclear receptor activity / positive regulation of fibroblast proliferation / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / 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 / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of gene expression / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / 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 / cytoplasm / cytosol
Similarity search - Function
Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / Estrogen receptor/oestrogen-related receptor / : / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor ...Oestrogen-type nuclear receptor final C-terminal domain / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor / : / Oestrogen receptor / 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
LSZ102 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
DepositionDec 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 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
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-10 kcal/mol
Surface area17690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.370, 53.676, 96.848
Angle α, β, γ (deg.)90.000, 113.740, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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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
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-C6V / LSZ102 / (2E)-3-[4-({2-[2-(1,1-difluoroethyl)-4-fluorophenyl]-6-hydroxy-1-benzothiophen-3-yl}oxy)phenyl]prop-2-enoic acid


Mass: 470.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H17F3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.09 Å3/Da / Density % sol: 41.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, TRIS pH 7.0, MgCl2

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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 CCD 165 mm / Detector: CCD / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28729 / % possible obs: 98.9 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.95 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 17.1
Reflection shellResolution: 2.1→2.4 Å / Rmerge(I) obs: 0.536 / Num. unique obs: 28729 / % possible all: 91.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PSJ

6psj


Resolution: 2.1→42.17 Å / SU ML: 0.248 / Cross valid method: THROUGHOUT / σ(F): 1.355 / Phase error: 27.399
RfactorNum. reflection% reflection
Rfree0.256 1166 4.945 %
Rwork0.207 22415 -
obs0.209 23581 81.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.91 Å2 / Biso mean: 42.94 Å2 / Biso min: 9.1 Å2
Refinement stepCycle: final / Resolution: 2.1→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3296 0 66 143 3505
Biso mean--32.99 38.78 -
Num. residues----424
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.11-2.19870.2997470.25161091113832
2.1987-2.31460.3405720.24251559163145
2.3146-2.45960.28441310.24582619275076
2.4596-2.64950.32131710.23853338350998
2.6495-2.91610.25771860.229334333619100
2.9161-3.33790.25041750.213834613636100
3.3379-4.20480.22592000.179634333633100
4.2048-42.16120.24371840.18823481366598
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)
16.8796-0.5598-0.75385.5317-2.68466.6382-0.08180.9679-0.1077-0.75250.06530.24130.1909-0.36520.02470.3259-0.0433-0.0970.48450.00520.2368.65214.538895.5522
26.3837-1.48131.78415.9431-1.7574.17070.0008-0.8203-0.7380.82850.22740.0967-0.01370.2046-0.17390.3554-0.12390.00110.37210.0680.362365.1932.7492119.3467
35.79191.2031-2.97125.1226-3.34344.9102-0.02090.2152-1.053-0.2840.0316-0.29670.5131-0.10530.06860.2087-0.11490.03650.2555-0.02490.436973.2131.4731109.8662
47.3096-0.9858-1.41255.517-0.3334.71460.23120.0489-1.0417-0.2653-0.5198-0.390.26330.10030.32770.197-0.12390.01950.20370.05080.361879.07325.6718110.0723
53.58644.099-3.67967.5503-2.44684.76430.5424-0.98710.63221.2839-0.59381.0904-0.1542-0.3087-0.06860.3844-0.1590.11360.5629-0.04390.348368.054512.5117125.3337
66.7607-1.7835-7.67578.25621.78758.7452-0.2929-2.08760.02851.9113-0.349-0.33570.3047-0.25580.65010.9268-0.241-0.06570.9477-0.03770.470177.489610.7851133.7414
75.096-5.48734.09836.1417-5.08728.75560.1964-1.55040.48020.6875-0.266-0.3426-0.0139-0.54290.03910.4274-0.2145-0.04290.467-0.04720.290177.82617.4778123.3668
87.1976-3.6287-3.48734.012.63035.3199-0.03680.15730.2131-0.13440.03980.0268-0.1284-0.29010.02010.1608-0.0656-0.01730.1960.04010.163574.245117.0452107.5404
92.93790.34041.70446.2926-1.26264.30960.38360.0605-0.4448-1.0887-0.0396-1.67640.11010.7213-0.33230.46640.05470.09050.51280.00190.672889.30077.7149101.0583
108.5119-2.6499-1.11446.41281.47757.1588-0.04980.8190.2073-0.80350.01520.3637-0.269-0.08090.010.2713-0.0884-0.07280.29730.07350.200676.016321.746898.4804
115.81220.12611.80686.1957-3.43516.32090.1644-0.4394-0.07640.607-0.5046-0.6046-0.30150.25980.32290.2012-0.1417-0.0210.25280.00860.24583.127618.1711113.2201
127.15250.16810.02272.94151.22354.73640.536-0.3463-1.9585-0.2751-1.5613-0.61143.2822-0.48330.99331.3908-0.1380.30730.5593-0.05131.502380.6138-6.1485110.4883
137.73180.8142-2.84561.4578-3.06619.65370.2059-0.08352.0474-0.46620.3057-0.4732-1.5278-0.2574-0.4920.6407-0.1054-0.03260.2850.17440.749595.962339.7785107.5447
146.7164-5.3403-1.80534.20661.44672.36830.01680.22550.09270.383-0.1111-0.45470.06740.38750.13910.2851-0.0873-0.01860.22170.08980.3917114.665419.2965111.6382
155.1535-4.6702-0.68575.12560.32093.55610.0615-0.4028-0.26790.1892-0.14770.1319-0.11990.5978-0.0450.1653-0.10370.00450.320.08080.2502109.143121.2032117.8042
163.005-2.1918-3.70965.52791.90589.18330.1041-0.9011.3440.36360.0982-0.0052-1.6289-0.3723-0.27390.38890.02890.05640.4052-0.15080.340294.536435.5675120.9998
175.5447-1.7178-0.38765.78663.24945.3273-0.0118-0.3807-0.25080.37360.00710.03080.1472-0.26750.07280.1772-0.109-0.01770.2460.0930.191298.790422.6551117.4524
182.032-2.17155.59193.69660.27143.78390.21631.6551-0.6751-0.4163-0.2874-0.37650.46980.5067-0.01220.3513-0.06430.17360.4966-0.0770.4334110.503214.295103.3674
196.84751.36842.06590.3150.94336.56390.07280.1113-2.56610.4760.5204-1.19372.1651.0885-0.55220.87690.0869-0.01490.5781-0.08851.4144108.36372.9819109.6871
207.2535-1.71961.23717.9806-0.08437.21170.19440.7961-1.3601-0.56250.20540.06360.44920.0163-0.34150.2874-0.1180.04990.3485-0.18040.490799.565611.599103.1031
216.9138-1.61172.09237.05823.28778.632-0.16830.23420.2579-0.13460.12340.35830.0957-0.34230.03090.222-0.1046-0.05620.19270.07450.25193.742926.3666108.6598
224.86151.0761.21984.01320.17992.8951-0.26020.24151.42250.16770.17790.1794-0.44220.06940.11140.4955-0.1961-0.00780.24860.30160.438987.736333.5934104.6389
236.3449-1.02553.59235.8383-3.2266.0983-0.00590.4332-0.48290.0361-0.0299-0.0739-0.17410.10480.04560.1938-0.09990.06050.22860.0290.233190.52818.0256106.7766
246.5496-4.5957-2.00625.84214.50644.2871-0.4933-0.6414-0.67541.48810.63890.1803-0.8240.387-0.17051.07350.338-0.13860.8507-0.05620.6359104.297712.073126.1942
255.833-1.3792-6.272.00972.88179.5866-0.024-1.78860.33780.94810.4336-0.99880.50840.8073-0.42160.53390.1623-0.0311.2420.01210.3465105.224428.6713128.8513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 306 THROUGH 321 )A0
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 322 THROUGH 341 )A0
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 342 THROUGH 371 )A0
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 372 THROUGH 394 )A0
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 395 THROUGH 411 )A0
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 412 THROUGH 420 )A0
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 421 THROUGH 437 )A0
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 438 THROUGH 455 )A0
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 456 THROUGH 473 )A0
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 474 THROUGH 496 )A0
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 497 THROUGH 526 )A0
12X-RAY DIFFRACTION12CHAIN 'A' AND (RESID 527 THROUGH 545 )A0
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 307 THROUGH 321 )B0
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 322 THROUGH 338 )B0
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 339 THROUGH 363 )B0
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 364 THROUGH 371 )B0
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 372 THROUGH 394 )B0
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 395 THROUGH 411 )B0
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 412 THROUGH 421 )B0
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 422 THROUGH 437 )B0
21X-RAY DIFFRACTION21CHAIN 'B' AND (RESID 438 THROUGH 473 )B0
22X-RAY DIFFRACTION22CHAIN 'B' AND (RESID 474 THROUGH 496 )B0
23X-RAY DIFFRACTION23CHAIN 'B' AND (RESID 497 THROUGH 525 )B0
24X-RAY DIFFRACTION24CHAIN 'B' AND (RESID 526 THROUGH 535 )B0
25X-RAY DIFFRACTION25CHAIN 'B' AND (RESID 536 THROUGH 544 )B0

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