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- PDB-5ufx: Estrogen Receptor Alpha Ligand Binding Domain in Complex with OP1074 -

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Basic information

Entry
Database: PDB / ID: 5ufx
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with OP1074
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Estrogen / Steroid / Acquired Resistance
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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / 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 / nuclear estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / uterus development / mammary gland branching involved in pregnancy / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / androgen metabolic process / cellular response to estrogen stimulus / mammary gland alveolus development / estrogen response element binding / Mitochondrial unfolded protein response (UPRmt) / nuclear receptor-mediated steroid hormone signaling pathway / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / protein localization to chromatin / estrogen receptor signaling pathway / negative regulation of canonical NF-kappaB signal transduction / steroid binding / 14-3-3 protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / TBP-class protein binding / nitric-oxide synthase regulator activity / positive regulation of nitric-oxide synthase activity / negative regulation of miRNA transcription / ESR-mediated signaling / positive regulation of DNA-binding transcription factor activity / transcription coregulator binding / transcription corepressor binding / nuclear estrogen receptor binding / negative regulation of DNA-binding transcription factor activity / stem cell differentiation / SUMOylation of intracellular receptors / cellular response to estradiol stimulus / transcription coactivator binding / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / nuclear receptor activity / positive regulation of fibroblast proliferation / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / response to estradiol / PIP3 activates AKT signaling / ATPase binding / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of inflammatory response / 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 / Extra-nuclear estrogen signaling / calmodulin binding / 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 / 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 / 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
Chem-86Y / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5503 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.
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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-13 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.722, 58.015, 87.834
Angle α, β, γ (deg.)90.00, 102.89, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1046-

HOH

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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-86Y / (2S)-3-(4-hydroxyphenyl)-4-methyl-2-(4-{2-[(3R)-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


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3,350, Bis-Tris pH 6.2, 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: 1.55→20 Å / Num. obs: 70195 / % possible obs: 96.2 % / Redundancy: 3.6 % / Net I/σ(I): 8.07
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 15.18 / CC1/2: 0.75 / % possible all: 99.9

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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: 1.5503→19.988 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.83
RfactorNum. reflection% reflection
Rfree0.2299 3441 5 %
Rwork0.1952 --
obs0.1969 68880 94.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5503→19.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3657 0 68 616 4341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073889
X-RAY DIFFRACTIONf_angle_d1.1215282
X-RAY DIFFRACTIONf_dihedral_angle_d14.5861430
X-RAY DIFFRACTIONf_chiral_restr0.042618
X-RAY DIFFRACTIONf_plane_restr0.004654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5503-1.57160.2769960.23992033X-RAY DIFFRACTION74
1.5716-1.5940.25341380.22612496X-RAY DIFFRACTION90
1.594-1.61780.27181340.23262696X-RAY DIFFRACTION97
1.6178-1.6430.23591430.21492732X-RAY DIFFRACTION99
1.643-1.670.26421400.20782749X-RAY DIFFRACTION100
1.67-1.69880.24731480.20382763X-RAY DIFFRACTION100
1.6988-1.72960.22521430.19382780X-RAY DIFFRACTION100
1.7296-1.76290.22351290.19642776X-RAY DIFFRACTION100
1.7629-1.79880.21661370.19452779X-RAY DIFFRACTION100
1.7988-1.83790.19741400.1942783X-RAY DIFFRACTION100
1.8379-1.88060.29251430.24462735X-RAY DIFFRACTION99
1.8806-1.92760.51031570.44532588X-RAY DIFFRACTION94
1.9276-1.97970.44331360.32262693X-RAY DIFFRACTION96
1.9797-2.03790.23081550.1942745X-RAY DIFFRACTION100
2.0379-2.10360.21121550.17582793X-RAY DIFFRACTION100
2.1036-2.17870.20021380.16982762X-RAY DIFFRACTION100
2.1787-2.26580.2434730.21041282X-RAY DIFFRACTION50
2.2658-2.36880.19961230.18162381X-RAY DIFFRACTION95
2.3688-2.49350.22741400.17572779X-RAY DIFFRACTION100
2.4935-2.64940.23751350.18122808X-RAY DIFFRACTION100
2.6494-2.85340.21521830.18052751X-RAY DIFFRACTION100
2.8534-3.13960.20971350.17542813X-RAY DIFFRACTION100
3.1396-3.59160.19431500.16632742X-RAY DIFFRACTION98
3.5916-4.51640.17081120.14672155X-RAY DIFFRACTION76
4.5164-19.99010.17911580.16762825X-RAY DIFFRACTION98
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)
16.093.4331-2.01195.4501-1.37032.8958-0.15490.40690.5621-0.27360.1960.1883-0.3451-0.0992-0.0740.34590.0151-0.05160.11120.05120.23968.4619-5.25217.7484
24.11811.3927-2.49663.8333-2.05314.63920.0043-0.11540.09430.15610.10.42770.1986-0.2553-0.10980.12360.05370.0050.1325-0.00720.1427-12.0942-22.492630.3969
33.87132.6376-1.91233.3419-1.74622.35330.03270.2151-0.0483-0.0328-0.05480.03730.0396-0.07270.02570.09010.0745-0.01760.1116-0.00770.0853-5.8497-24.564421.3429
41.83320.3648-0.56490.816-0.33463.1237-0.02350.0156-0.07390.00810.0084-0.02120.033-0.07780.02090.06880.0488-0.0170.058-0.00390.0831.6378-24.924224.9691
55.29183.815-0.3392.7597-0.35842.9484-0.0213-0.2705-0.3186-0.057-0.0178-0.25750.25730.1749-0.01730.13850.0686-0.01080.12690.02030.10987.6961-27.466935.4955
61.46640.85690.8031.4887-0.18084.5296-0.03230.1397-0.0126-0.1353-0.0141-0.1010.07830.1597-0.01930.08910.0467-0.00010.09860.01060.100411.233-19.104619.7197
72.42990.90231.86153.28452.53128.0936-0.04460.24840.2928-0.14220.0502-0.2044-0.27670.0470.00860.13590.0422-0.0120.12170.06240.156617.4346-13.068415.0916
83.66393.02840.42825.82780.70391.0407-0.0096-0.0833-0.1320.0474-0.0774-0.01020.05660.0470.08670.10050.0708-0.00240.09060.0010.107413.389-26.244726.6265
93.2242.46722.4844.29460.22883.11790.07040.4297-0.44360.3250.160.2834-0.08070.0789-0.15130.4305-0.10830.05850.47-0.19170.4045-4.3908-37.393715.6172
101.1191-0.16461.14141.7232-1.96315.162-0.01570.3261-0.0512-0.296-0.02590.15990.2408-0.4889-0.0880.2978-0.1605-0.00720.7278-0.05240.1446-4.417-24.67745.7134
111.9586-0.03090.46715.3810.69851.50130.04860.11070.10590.017-0.0139-0.38930.05090.1246-0.00070.11560.05890.02540.19820.07070.222138.1239-37.287923.2512
123.23180.58780.94946.82663.62953.52230.06950.2061-0.168-0.1363-0.1023-0.03920.07630.04310.01180.08570.07690.01520.14140.03950.109731.7987-44.774224.845
131.2779-0.24710.45781.8523-0.25352.33010.0548-0.02230.05040.0801-0.0864-0.0539-0.0184-0.02990.04180.09770.07210.00440.10980.01580.100627.1287-36.283630.7345
141.2691-0.2729-0.89141.51760.15320.98560.12390.5525-0.1487-0.5281-0.27750.1390.0283-0.29810.19330.32380.24890.04710.4357-0.04550.1528.0127-42.93018.1376
152.33691.2320.8395.3940.44752.9510.16630.32130.091-0.7703-0.22280.1482-0.1513-0.25720.02880.29110.1855-0.00740.38890.03210.140323.2208-33.752110.5104
162.29250.55610.19633.4121-1.21292.27260.20740.11550.4139-0.1238-0.1565-0.1322-0.1705-0.0533-0.05320.13910.08090.02160.13920.02590.172327.9085-27.947126.3277
173.4880.7403-1.10836.0478-3.87747.2354-0.0501-0.29290.31860.2827-0.0502-0.3163-0.06560.3610.05430.11040.0445-0.03210.2017-0.00230.209630.0327-19.555230.7656
182.01032.18730.12858.7733-0.45120.91620.06640.1944-0.0904-0.1548-0.0977-0.09020.03270.0650.02890.10620.08210.01040.1327-0.00060.096520.3441-29.408419.9355
198.25492.44087.73325.31693.35739.49160.39350.1746-0.8648-0.4151-0.12320.24131.0262-0.1545-0.35250.2583-0.0086-0.05270.2492-0.00470.264519.0969-51.119827.439
208.46410.16731.1347.11220.65265.11090.0852-0.2809-0.13390.3355-0.1379-0.3068-0.02260.39450.06530.160.0317-0.00120.17580.05380.076430.04-45.975839.0069
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 363 )
4X-RAY DIFFRACTION4chain 'A' and (resid 364 through 420 )
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 438 )
6X-RAY DIFFRACTION6chain 'A' and (resid 439 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 306 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 420 )
15X-RAY DIFFRACTION15chain 'B' and (resid 421 through 438 )
16X-RAY DIFFRACTION16chain 'B' and (resid 439 through 469 )
17X-RAY DIFFRACTION17chain 'B' and (resid 470 through 496 )
18X-RAY DIFFRACTION18chain 'B' and (resid 497 through 528 )
19X-RAY DIFFRACTION19chain 'B' and (resid 529 through 536 )
20X-RAY DIFFRACTION20chain 'B' and (resid 537 through 547 )

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