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- PDB-5ufw: Estrogen Receptor Alpha Ligand Binding Domain in Complex with OP1154 -

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Basic information

Entry
Database: PDB / ID: 5ufw
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with OP1154
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Estrogen / Breast Cancer / Hormone / Nuclear Hormone Receptor
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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / intracellular steroid hormone receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / transcription corepressor binding / negative regulation of miRNA transcription / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of nitric-oxide synthase activity / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / chromatin / regulation of DNA-templated transcription / 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 / membrane / identical protein binding / 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 / Nuclear hormones receptors DNA-binding region signature. ...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
Chem-86V / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.583 Å
AuthorsFanning, S.W. / Hodges-Gallagher, L. / Myles, D.C. / Sun, R. / Fowler, C.E. / Green, B.D. / Harmon, C.L. / Greene, G.L. / Kushner, P.J.
Funding support United States, 2items
OrganizationGrant numberCountry
Susan G. Komen FoundationPDF14301382 United States
Ludwig Fund for Metastasis Research United States
CitationJournal: Nat Commun / Year: 2018
Title: Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity.
Authors: Fanning, S.W. / Hodges-Gallagher, L. / Myles, D.C. / Sun, R. / Fowler, C.E. / Plant, I.N. / Green, B.D. / Harmon, C.L. / Greene, G.L. / Kushner, P.J.
History
DepositionJan 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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
B: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,6264
Polymers56,7102
Non-polymers9152
Water11,223623
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-14 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.569, 57.878, 87.701
Angle α, β, γ (deg.)90.00, 102.91, 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: 28355.207 Da / Num. of mol.: 2 / Mutation: C381S, C417S, C530S, L536S
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-86V / (2S)-3-(4-hydroxyphenyl)-4-methyl-2-(4-{2-[(3S)-3-methylpyrrolidin-1-yl]ethoxy}phenyl)-2H-1-benzopyran-7-ol


Mass: 457.561 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H31NO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3,350, Tris pH 7.5, and 200 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.58→20 Å / Num. obs: 68281 / % possible obs: 99.7 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 3.6
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 2.9 % / Num. unique obs: 3258 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIX1.9_1692data reduction
PHENIX1.9_1692data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ACC

5acc


Resolution: 1.583→19.952 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 3366 5.07 %
Rwork0.1797 --
obs0.1813 66450 97.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.583→19.952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 68 623 4384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053975
X-RAY DIFFRACTIONf_angle_d0.8775408
X-RAY DIFFRACTIONf_dihedral_angle_d14.4051473
X-RAY DIFFRACTIONf_chiral_restr0.032626
X-RAY DIFFRACTIONf_plane_restr0.004677
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5827-1.60530.23031030.2311740X-RAY DIFFRACTION65
1.6053-1.62920.27261200.23192184X-RAY DIFFRACTION81
1.6292-1.65470.26761180.21862485X-RAY DIFFRACTION91
1.6547-1.68180.22961310.21462631X-RAY DIFFRACTION98
1.6818-1.71080.2241400.19392685X-RAY DIFFRACTION100
1.7108-1.74190.21191240.20082714X-RAY DIFFRACTION100
1.7419-1.77540.25131250.20152716X-RAY DIFFRACTION100
1.7754-1.81160.2221310.19682668X-RAY DIFFRACTION100
1.8116-1.85090.2281410.19762699X-RAY DIFFRACTION100
1.8509-1.8940.30471540.24132675X-RAY DIFFRACTION100
1.894-1.94130.28111540.25462678X-RAY DIFFRACTION100
1.9413-1.99370.22351460.21922697X-RAY DIFFRACTION100
1.9937-2.05230.23421460.17582686X-RAY DIFFRACTION100
2.0523-2.11850.21221450.17142695X-RAY DIFFRACTION100
2.1185-2.19410.19551470.17862703X-RAY DIFFRACTION100
2.1941-2.28190.25951490.21062689X-RAY DIFFRACTION99
2.2819-2.38560.23231500.18692681X-RAY DIFFRACTION100
2.3856-2.51110.17271360.1652698X-RAY DIFFRACTION100
2.5111-2.66810.20361420.16882730X-RAY DIFFRACTION100
2.6681-2.87360.18131350.1692702X-RAY DIFFRACTION100
2.8736-3.16170.20811320.16512733X-RAY DIFFRACTION100
3.1617-3.61690.19211900.15842691X-RAY DIFFRACTION100
3.6169-4.54790.17591660.14062725X-RAY DIFFRACTION100
4.5479-19.95320.1881410.16792779X-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)
18.16185.6683-2.49128.573-2.79372.7975-0.11890.44660.5012-0.3590.16050.1315-0.2731-0.0979-0.04910.29750.0145-0.04340.11370.04890.19598.4915-4.990817.7869
22.67640.5069-2.22980.5247-0.74633.8359-0.1038-0.0146-0.16910.0560.00860.2070.3643-0.36880.08730.13640.02920.02090.12450.00240.2196-13.3491-23.168730.9214
31.67750.3629-0.29090.5892-0.12041.2613-0.0140.1042-0.0355-0.01790.01720.007-0.0543-0.0634-0.0080.08410.0585-0.00930.07070.00060.0721-0.5259-23.272222.495
43.4899-0.4483-1.78451.23242.78086.5963-0.0978-0.1672-0.48120.4021-0.0974-0.13691.0208-0.16460.18650.3344-0.04640.00380.23180.09460.2846-2.2785-37.95537.732
54.16032.9567-0.20429.2733-0.14082.7012-0.0208-0.2896-0.3153-0.0006-0.0198-0.13070.2990.16850.01550.13470.08590.01240.12860.03060.06797.1816-27.95135.463
61.19870.47250.06311.54150.92795.3157-0.02450.10830.0143-0.07740.0214-0.07020.13810.1705-0.04250.10210.0566-0.0070.09190.0040.084211.5502-19.338119.7816
71.93830.7271.32613.22452.68586.8601-0.02730.26250.2573-0.15780.0635-0.174-0.21830.0137-0.0210.13650.0394-0.0170.13180.05870.145217.2546-13.171314.4691
83.4992.72010.72314.43110.7730.9765-0.018-0.1069-0.10890.06-0.05390.03530.07580.07380.06650.11340.07560.00050.1054-0.00090.091213.8225-25.600426.6651
93.58613.4924-5.08573.4235-4.94547.237-0.10040.3005-0.183-0.51170.45080.04860.3269-0.0385-0.30650.34870.00450.0050.345-0.09760.3165-4.0618-36.819615.8217
100.938-0.70471.55462.4841-1.555.45490.04560.1034-0.0426-0.4218-0.02760.140.216-0.3145-0.05930.3093-0.1204-0.01160.6774-0.02650.1184-4.4516-24.47915.7334
112.01121.74131.2516.18852.42345.8721-0.2219-0.24670.05780.56210.0596-0.581-0.19390.21940.16220.2160.0202-0.08210.20640.02680.348440.0079-23.325931.8
120.56050.0649-0.54771.407-0.93141.09630.04320.3487-0.2968-0.6512-0.05890.02860.4139-0.18750.1540.34310.11-0.00030.249-0.02510.363136.3119-50.274714.4464
132.34630.58280.74664.85212.69832.92780.07850.1114-0.1193-0.1499-0.1476-0.06520.01970.02420.05620.09320.08040.010.14390.03460.108831.7296-44.49524.8032
141.05880.2370.16431.5871-0.23711.50010.1038-0.04990.06620.1242-0.1235-0.0372-0.0523-0.01280.04410.11380.07110.01010.11220.01550.095326.8689-36.122330.9637
151.1129-0.253-1.00420.92910.14850.98450.06650.4959-0.0769-0.458-0.23560.1020.0262-0.24540.0890.32780.26910.05350.4282-0.03460.107328.5261-42.22788.2928
162.85422.37820.96125.8590.74893.31220.0880.29860.1123-0.6627-0.0750.1695-0.1295-0.1965-0.01810.28730.1718-0.01060.33980.02780.128523.1908-33.402210.4542
172.0050.2796-0.17282.3031-0.35672.87260.14270.01640.2799-0.0102-0.0916-0.022-0.0693-0.1023-0.04330.13260.08170.01140.14250.03430.160927.6423-27.851327.3034
181.34970.24520.31012.77740.02790.83360.01080.05250.0588-0.0801-0.1022-0.1276-0.00330.11140.090.08760.07170.01570.14390.02190.09824.4877-24.474523.8751
194.99624.62085.52775.52945.56756.41490.3357-0.0745-0.61840.00850.00470.25570.6068-0.2422-0.34560.17560.041-0.03540.28880.03870.280918.9104-50.976727.3423
205.40822.29580.54464.29130.8574.6250.1213-0.1742-0.19350.2423-0.095-0.2052-0.00020.1766-0.02530.1550.03990.00710.15320.04760.081229.5667-46.008138.4301
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 309 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 338 )
3X-RAY DIFFRACTION3chain 'A' and (resid 339 through 411 )
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 420 )
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 437 )
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 465 )
7X-RAY DIFFRACTION7chain 'A' and (resid 466 through 496 )
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 528 )
9X-RAY DIFFRACTION9chain 'A' and (resid 529 through 536 )
10X-RAY DIFFRACTION10chain 'A' and (resid 537 through 547 )
11X-RAY DIFFRACTION11chain 'B' and (resid 307 through 321 )
12X-RAY DIFFRACTION12chain 'B' and (resid 322 through 341 )
13X-RAY DIFFRACTION13chain 'B' and (resid 342 through 363 )
14X-RAY DIFFRACTION14chain 'B' and (resid 364 through 394 )
15X-RAY DIFFRACTION15chain 'B' and (resid 395 through 420 )
16X-RAY DIFFRACTION16chain 'B' and (resid 421 through 438 )
17X-RAY DIFFRACTION17chain 'B' and (resid 439 through 471 )
18X-RAY DIFFRACTION18chain 'B' and (resid 472 through 528 )
19X-RAY DIFFRACTION19chain 'B' and (resid 529 through 536 )
20X-RAY DIFFRACTION20chain 'B' and (resid 537 through 546 )

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