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- PDB-7ujy: Estrogen receptor alpha ligand binding domain Y537S mutant in com... -

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Basic information

Entry
Database: PDB / ID: 7ujy
TitleEstrogen receptor alpha ligand binding domain Y537S mutant in complex with a methylated lasofoxifene derivative that enhances estrogen receptor alpha nuclear resonance time
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / ESTROGEN RECEPTOR ALPHA / DRUG RESISTANCE / BREAST CANCER / ALP HELICAL BUNDLE / ANTIESTROGEN / SERM
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / nuclear estrogen receptor activity / epithelial cell proliferation involved in mammary gland duct elongation / epithelial cell development / prostate epithelial cord elongation / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / TFIIB-class transcription factor binding / androgen metabolic process / steroid hormone receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / 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 / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid 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 / SUMOylation of intracellular receptors / euchromatin / negative regulation of DNA-binding transcription factor activity / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / regulation of inflammatory response / fibroblast proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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 / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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 / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) ...Estrogen receptor / Oestrogen-type nuclear receptor final C-terminal domain / : / Oestrogen receptor / Oestrogen-type nuclear receptor final C-terminal / Estrogen receptor/oestrogen-related 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
Similarity search - Domain/homology
Chem-RL4 / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHosfield, D.J. / Greene, G.L. / Fanning, S.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
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
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
SupersessionJun 15, 2022ID: 6VPK
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
B: Estrogen receptor
A: Estrogen receptor
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2998
Polymers120,5894
Non-polymers1,7104
Water11,385632
1
B: Estrogen receptor
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1504
Polymers60,2942
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-12 kcal/mol
Surface area20420 Å2
MethodPISA
2
C: Estrogen receptor
D: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1504
Polymers60,2942
Non-polymers8552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-12 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.343, 58.343, 274.652
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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


Mass: 30147.186 Da / Num. of mol.: 4 / Mutation: Y537S
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-RL4 / (5R,6S)-5-(4-{2-[(2R)-2-methylpyrrolidin-1-yl]ethoxy}phenyl)-6-phenyl-5,6,7,8-tetrahydronaphthalen-2-ol


Mass: 427.578 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H33NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.24 Å3/Da / Density % sol: 45.04 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3,350, Tris pH 7.5, MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 105602 / % possible obs: 99 % / Redundancy: 4 % / Rpim(I) all: 0.081 / Net I/σ(I): 20
Reflection shellResolution: 1.7→1.72 Å / Num. unique obs: 4200 / CC1/2: 0.51

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6VIG

6vig
PDB Unreleased entry


Resolution: 1.7→49.69 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.224 5294 5.01 %
Rwork0.188 100308 -
obs0.19 105602 91.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.55 Å2 / Biso mean: 21.85 Å2 / Biso min: 1.66 Å2
Refinement stepCycle: final / Resolution: 1.7→49.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7262 0 128 633 8023
Biso mean--20 27.87 -
Num. residues----920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.701-1.72010.3581560.25891134119030
1.7201-1.74030.2716700.24831425149540
1.7403-1.76150.2842890.24351771186049
1.7615-1.78380.25891250.22542328245364
1.7838-1.80730.25871700.2322955312582
1.8073-1.83210.29621580.24723490364895
1.8321-1.85820.22922070.22213576378399
1.8582-1.8860.26992080.220937003908100
1.886-1.91540.25151730.21835483721100
1.9154-1.94690.25551920.214437583950100
1.9469-1.98040.26051930.19335763769100
1.9804-2.01640.2371940.202636773871100
2.0164-2.05520.23781900.195435623752100
2.0552-2.09720.23742120.192736443856100
2.0972-2.14280.23061720.180736663838100
2.1428-2.19260.23161900.173836073797100
2.1926-2.24750.21232000.179337133913100
2.2475-2.30820.20371820.170435743756100
2.3082-2.37610.19851910.178536163807100
2.3761-2.45280.22422180.171636543872100
2.4528-2.54050.21052090.179436493858100
2.5405-2.64220.25632080.188936153823100
2.6422-2.76240.23841780.187836513829100
2.7624-2.90810.22091860.196136383824100
2.9081-3.09020.22381630.189936743837100
3.0902-3.32880.21211780.188435993777100
3.3288-3.66370.19692140.171436393853100
3.6637-4.19360.19572040.161736293833100
4.1936-5.28260.19321780.165336473825100
5.2826-49.60.23631860.20573593377999
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)
12.57371.09450.43613.10480.8781.8784-0.14980.0464-0.0853-0.10840.0541-0.2580.20.21810.08070.15240.10390.01320.09660.02390.1286-19.343-3.26619.226
20.9467-0.1781-0.15361.72380.1181.84880.06540.13060.003-0.2169-0.1355-0.05850.13880.03550.06080.19920.1112-0.00090.00320.00640.0869-24.372.6216.7
39.94366.36261.5178.35050.83972.9156-0.14360.52080.1228-0.49980.12620.0786-0.00130.04770.00230.20590.0707-0.0010.14830.01540.0757-26.2689.5155.837
41.91770.4101-0.32721.8852-0.73453.0406-0.0392-0.22430.15260.15280.0033-0.1381-0.04140.13580.03020.110.0499-0.0410.08770.00210.1345-20.64512.18823.779
53.34630.7-2.43022.2226-0.58895.21120.0222-0.10420.150.2497-0.0227-0.34930.03410.4741-0.01670.09010.0084-0.07660.13660.00090.1934-14.01317.75227.482
67.353.6163-0.73146.0784-0.93662.24320.02710.0956-0.0173-0.0509-0.11860.15830.05060.01940.06830.09410.0989-0.00140.0449-0.00230.0551-26.86113.84215.539
74.9402-2.29930.95563.0608-1.01613.37490.0231-0.1201-0.2959-0.01950.04540.12130.3494-0.0868-0.07490.4537-0.02070.01190.1659-0.01560.1384-26.019-5.32734.411
83.7130.0933-0.71691.87190.41691.8306-0.0716-0.1960.2565-0.039-0.0771-0.0036-0.268-0.09120.1530.19790.0926-0.04260.05460.00390.1339-41.64935.26218.277
91.2276-0.5772-0.45271.16470.18982.0973-0.1583-0.06610.06840.21330.0402-0.0263-0.1059-0.10320.0570.16540.1332-0.00960.0691-0.01220.0872-39.32427.83719.969
109.8285.8906-2.66587.3301-1.73824.73150.0112-0.2101-0.03060.155-0.01570.06110.0903-0.056-0.00070.17930.0642-0.01020.0908-0.00010.0639-34.97722.68731.183
112.1386-0.20940.33240.7466-0.13553.25980.03880.18320.1427-0.0606-0.0553-0.2358-0.14510.1503-0.00810.13550.0060.01080.05260.04050.1619-24.38628.41611.677
125.87693.62871.03214.44310.32541.8984-0.0991-0.0229-0.01280.08590.02240.0181-0.02770.0210.06590.13450.0542-0.00270.0226-0.00460.0747-29.00120.821.886
135.9913.0736-0.58372.0029-2.71434.71810.0170.1679-0.0427-0.05880.17960.47720.0887-0.4877-0.20090.2430.1560.01890.39570.02490.1257-47.21426.2475.269
142.43890.00430.39041.73340.14161.19560.06680.1204-0.291-0.0311-0.0874-0.01470.3171-0.09020.00740.2168-0.08040.01490.0685-0.00130.1327-12.50515.08665.014
151.08820.65650.01591.34520.11352.2944-0.014-0.1451-0.06280.026-0.0355-0.0650.1606-0.01910.04680.1114-0.06180.00320.06160.02110.0867-7.3123.04671.638
161.26181.451-0.07791.9238-0.24963.0613-0.2260.32330.1164-0.45810.12870.132-0.0178-0.31080.09730.3747-0.2946-0.0220.184-0.0940.1137-14.94123.06949.556
171.63540.46060.7311.6245-0.22882.9461-0.08410.069-0.0197-0.08980.0343-0.1195-0.1129-0.00370.03720.1441-0.03690.01480.05550.00550.1154-2.30325.58861.945
183.2425-1.2118-2.42482.60892.40745.77890.061-0.2767-0.19360.10570.0187-0.34160.41090.3897-0.10460.13810.027-0.04470.11130.06680.21778.53420.87873.491
199.9829-2.6448-1.30314.07570.12011.9319-0.0882-0.03290.1132-0.13520.01910.01080.01690.05590.05550.138-0.05420.00140.01230.00250.04650.30229.80760.972
202.32290.3079-1.42172.0046-5.61756.4701-0.0355-0.1987-0.1655-0.17160.22140.65740.2379-0.6234-0.2050.2605-0.1418-0.04130.4515-0.02210.1903-17.93620.73779.102
213.2276-2.27-1.45943.85652.03732.535-0.08310.1720.0769-0.07760.0615-0.431-0.17940.40280.02750.1367-0.09440.00520.23290.0470.274317.08448.55261.847
222.16150.01051.38082.68442.50133.1996-0.3272-0.4450.57030.54020.15390.123-0.5653-0.15440.17130.51280.0677-0.08850.2673-0.0760.3599-1.06467.51178.655
233.217-1.1014-1.12384.13781.70962.1621-0.0892-0.05050.15510.0226-0.03460.0236-0.05-0.03720.07810.1793-0.1149-0.01770.0421-0.00590.08384.77155.21762.257
240.72660.0903-0.39211.7883-0.24052.04240.03420.0828-0.0344-0.214-0.0461-0.0678-0.02480.06370.020.1442-0.05920.01480.05010.00690.08435.55845.32356.731
251.28941.3949-0.30962.6407-2.0192.5770.1689-0.2031-0.09180.5428-0.1442-0.0438-0.25720.072-0.03450.4953-0.256-0.14090.1402-0.04910.07326.01352.36678.666
263.0706-1.914-1.536.941.24543.1253-0.0251-0.21030.2570.5483-0.01320.1998-0.3365-0.08540.05190.2754-0.0820.01120.16440.00310.1143-0.6644.48778.055
272.2068-0.25330.83321.9609-0.23754.4194-0.00330.0695-0.1795-0.07060.0254-0.13980.04290.0615-0.03250.0968-0.04840.02650.07180.01360.12179.16838.29460.774
282.7945-1.14812.6022.1803-1.16545.30510.06590.049-0.1309-0.2328-0.0046-0.31030.01260.449-0.07950.0806-0.01390.07490.14870.00580.212115.24632.76155.454
297.7253-3.96631.415.2378-1.40261.9730.0157-0.13380.00120.0898-0.06150.0763-0.01260.02770.03110.1036-0.08430.01010.06350.00270.05713.07935.91567.682
307.1080.8503-3.02623.4505-0.59637.28480.20870.21680.4034-0.0304-0.04350.1831-0.5276-0.4461-0.16550.46740.02680.02610.15390.01030.1188-0.26554.02750.323
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 307:363 )A307 - 363
2X-RAY DIFFRACTION2( CHAIN A AND RESID 364:421 )A364 - 421
3X-RAY DIFFRACTION3( CHAIN A AND RESID 422:438 )A422 - 438
4X-RAY DIFFRACTION4( CHAIN A AND RESID 439:465 )A439 - 465
5X-RAY DIFFRACTION5( CHAIN A AND RESID 466:496 )A466 - 496
6X-RAY DIFFRACTION6( CHAIN A AND RESID 497:528 )A497 - 528
7X-RAY DIFFRACTION7( CHAIN A AND RESID 535:545 )A535 - 545
8X-RAY DIFFRACTION8( CHAIN B AND RESID 307:363 )B307 - 363
9X-RAY DIFFRACTION9( CHAIN B AND RESID 364:416 )B364 - 416
10X-RAY DIFFRACTION10( CHAIN B AND RESID 421:438 )B421 - 438
11X-RAY DIFFRACTION11( CHAIN B AND RESID 439:496 )B439 - 496
12X-RAY DIFFRACTION12( CHAIN B AND RESID 497:527 )B497 - 527
13X-RAY DIFFRACTION13( CHAIN B AND RESID 528:545 )B528 - 545
14X-RAY DIFFRACTION14( CHAIN C AND RESID 307:363 )C307 - 363
15X-RAY DIFFRACTION15( CHAIN C AND RESID 364:394 )C364 - 394
16X-RAY DIFFRACTION16( CHAIN C AND RESID 395:420 )C395 - 420
17X-RAY DIFFRACTION17( CHAIN C AND RESID 421:465 )C421 - 465
18X-RAY DIFFRACTION18( CHAIN C AND RESID 466:496 )C466 - 496
19X-RAY DIFFRACTION19( CHAIN C AND RESID 497:526 )C497 - 526
20X-RAY DIFFRACTION20( CHAIN C AND RESID 527:550 )C527 - 550
21X-RAY DIFFRACTION21( CHAIN D AND RESID 307:331 )D307 - 331
22X-RAY DIFFRACTION22( CHAIN D AND RESID 332:341 )D332 - 341
23X-RAY DIFFRACTION23( CHAIN D AND RESID 342:363 )D342 - 363
24X-RAY DIFFRACTION24( CHAIN D AND RESID 364:394 )D364 - 394
25X-RAY DIFFRACTION25( CHAIN D AND RESID 395:411 )D395 - 411
26X-RAY DIFFRACTION26( CHAIN D AND RESID 412:437 )D412 - 437
27X-RAY DIFFRACTION27( CHAIN D AND RESID 438:465 )D438 - 465
28X-RAY DIFFRACTION28( CHAIN D AND RESID 466:496 )D466 - 496
29X-RAY DIFFRACTION29( CHAIN D AND RESID 497:527 )D497 - 527
30X-RAY DIFFRACTION30( CHAIN D AND RESID 528:545 )D528 - 545

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