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- PDB-7r62: Estrogen Receptor Alpha Ligand Binding Domain in Complex with a D... -

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Basic information

Entry
Database: PDB / ID: 7r62
TitleEstrogen Receptor Alpha Ligand Binding Domain in Complex with a Desmethyl ICI164,384 Derivative
ComponentsEstrogen receptor
KeywordsTRANSCRIPTION / Breast Cancer / Selective Estrogen Receptor Degrader / Alpha Helical Bundle / Antiestrogen
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
Chem-3YJ / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsDiennet, M. / El Ezzy, M. / Thiombane, K. / Cotnoir-White, D. / Poupart, J. / Gao, Z. / Mendoza Sanchez, R. / Marinier, A. / Gleason, J. / Greene, G.L. ...Diennet, M. / El Ezzy, M. / Thiombane, K. / Cotnoir-White, D. / Poupart, J. / Gao, Z. / Mendoza Sanchez, R. / Marinier, A. / Gleason, J. / Greene, G.L. / Mader, S.C. / Fanning, S.W.
CitationJournal: To Be Published
Title: Estrogen Receptor Alpha Ligand Binding Domain in Complex with a Desmethyl ICI164,384 Derivative
Authors: Fanning, S.W.
History
DepositionJun 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 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
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8672
Polymers28,3551
Non-polymers5121
Water4,954275
1
A: Estrogen receptor
hetero molecules

A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7344
Polymers56,7102
Non-polymers1,0242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_445-y-1,-x-1,-z+1/61
Buried area3000 Å2
ΔGint-12 kcal/mol
Surface area20540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.709, 58.709, 274.292
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-770-

HOH

21A-777-

HOH

31A-959-

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.: 1
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-3YJ / 11-[3,17beta-dihydroxyestra-1,3,5(10)-trien-7beta-yl]-N-methyl-N-propylundecanamide


Mass: 511.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H53NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Magnesium Chloride

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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: Jun 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→47.67 Å / Num. obs: 41636 / % possible obs: 89.77 % / Redundancy: 10 % / CC1/2: 0.99 / Net I/σ(I): 24590
Reflection shellResolution: 1.5→1.554 Å / Num. unique obs: 2288 / CC1/2: 0.635

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UFX

5ufx


Resolution: 1.5→47.67 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 2103 5.05 %
Rwork0.2009 39533 -
obs0.2023 41636 89.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.98 Å2 / Biso mean: 23.1061 Å2 / Biso min: 4.82 Å2
Refinement stepCycle: final / Resolution: 1.5→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1857 0 37 275 2169
Biso mean--26.06 31.04 -
Num. residues----234
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.530.2748730.25551270134345
1.53-1.570.3108970.24171794189162
1.57-1.610.25541490.22742278242780
1.61-1.660.24621310.22322512264387
1.66-1.710.21741330.22212663279692
1.71-1.780.24611640.21232757292196
1.78-1.850.23841430.21312832297597
1.85-1.930.21161630.21642818298198
1.93-2.030.23811490.20732902305198
2.03-2.160.22441290.19812883301298
2.16-2.330.22481430.18682852299597
2.33-2.560.21451630.19452854301796
2.56-2.930.25191660.22859302596
2.93-3.690.20161450.18662989313497
3.69-47.670.23411550.19573270342599
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)
14.6012-0.7174-0.01623.6068-1.20732.6491-0.0688-0.24260.17280.10880.0068-0.4537-0.51380.13750.03650.1546-0.114-0.09230.08040.04120.1571-17.9094.441226.3202
24.8549-2.921-3.7165.14962.75594.566-0.17240.1130.0392-0.11960.0420.0009-0.0378-0.0510.10050.1412-0.0603-0.01730.0663-0.00130.0774-24.65974.765320.713
30.5154-0.25760.05941.98681.12793.97530.1570.1062-0.0238-0.2968-0.1228-0.1380.14220.0651-0.02560.1884-0.04110.03550.05550.00620.0797-23.6122-5.399915.5141
43.5155-0.29330.11193.21460.47782.3973-0.2734-0.8389-0.38081.1170.04340.36060.052-0.09590.12140.3807-0.11460.03020.1735-0.04510.0222-27.80251.295137.4501
55.3066-2.7685-1.3894.56270.33962.4224-0.2305-0.4403-0.25110.76590.15050.15890.23710.02790.07440.2787-0.07350.00840.15410.00940.1127-25.9058-9.684535.7203
62.5969-1.0466-1.47363.50550.30492.97870.13330.2859-0.2635-0.2067-0.1039-0.12160.1145-0.16050.06460.1586-0.04210.03650.0574-0.00310.1375-20.5459-12.24417.7719
73.5692-1.29233.21423.6316-1.61477.86220.10140.1087-0.1655-0.6028-0.1049-0.7707-0.05110.3309-0.0590.1912-0.03760.10940.11040.00360.2443-13.9319-17.926213.9002
87.6948-5.08980.76087.035-0.42910.95210.0683-0.1684-0.10660.1208-0.04760.13920.0178-0.0028-0.0380.1169-0.08030.00920.07970.00470.0868-25.9713-14.876426.1972
98.0513.6759-7.22374.8989-2.71058.5753-0.54080.11280.29570.03630.3860.25240.0288-0.32180.25490.55860.06790.00990.29170.07040.2535-28.67393.92598.9279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 311 through 341 )A311 - 341
2X-RAY DIFFRACTION2chain 'A' and (resid 342 through 363 )A342 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 394 )A364 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 420 )A395 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 438 )A421 - 438
6X-RAY DIFFRACTION6chain 'A' and (resid 439 through 465 )A439 - 465
7X-RAY DIFFRACTION7chain 'A' and (resid 466 through 496 )A466 - 496
8X-RAY DIFFRACTION8chain 'A' and (resid 497 through 528 )A497 - 528
9X-RAY DIFFRACTION9chain 'A' and (resid 529 through 548 )A529 - 548

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