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- PDB-7jhd: Estrogen Receptor Alpha Ligand Binding Domain Y537S in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 7jhd
TitleEstrogen Receptor Alpha Ligand Binding Domain Y537S in Complex with TTC-352 and GRIP Peptide
Components
  • Estrogen receptor
  • Nuclear receptor coactivator 2
KeywordsTRANSCRIPTION / Breast Cancer / Synthetic Agonist / Drug Resistance / Apoptosis
Function / homology
Function and homology information


regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / regulation of toll-like receptor signaling pathway ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / prostate epithelial cord elongation / 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 proliferation involved in mammary gland duct elongation / epithelial cell development / vagina development / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / 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 / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / SUMOylation of transcription cofactors / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Regulation of RUNX2 expression and activity / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / regulation of inflammatory response / positive regulation of cytosolic calcium ion concentration / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific
Similarity search - Function
Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 ...Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / 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 receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / PAS domain / : / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / 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-V9J / Estrogen receptor / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 Å
AuthorsFanning, S.W. / Abderraman, B. / Maximov, P.Y. / Jordan, V.C. / Greene, G.L.
CitationJournal: Mol.Cancer Ther. / Year: 2021
Title: Rapid Induction of the Unfolded Protein Response and Apoptosis by Estrogen Mimic TTC-352 for the Treatment of Endocrine-Resistant Breast Cancer.
Authors: Abderrahman, B. / Maximov, P.Y. / Curpan, R.F. / Fanning, S.W. / Hanspal, J.S. / Fan, P. / Foulds, C.E. / Chen, Y. / Malovannaya, A. / Jain, A. / Xiong, R. / Greene, G.L. / Tonetti, D.A. / ...Authors: Abderrahman, B. / Maximov, P.Y. / Curpan, R.F. / Fanning, S.W. / Hanspal, J.S. / Fan, P. / Foulds, C.E. / Chen, Y. / Malovannaya, A. / Jain, A. / Xiong, R. / Greene, G.L. / Tonetti, D.A. / Thatcher, G.R.J. / Jordan, V.C.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 10, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.3Oct 18, 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
C: Nuclear receptor coactivator 2
D: Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0086
Polymers60,3034
Non-polymers7052
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-29 kcal/mol
Surface area18280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.030, 82.436, 58.677
Angle α, β, γ (deg.)90.000, 110.750, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28571.660 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: Protein/peptide Nuclear receptor coactivator 2 / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 1579.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCOA2, BHLHE75, SRC2, TIF2 / Production host: synthetic construct (others) / References: UniProt: Q15596
#3: Chemical ChemComp-V9J / 3-(4-fluorophenyl)-2-(4-hydroxyphenoxy)-1-benzothiophene-6-ol


Mass: 352.379 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H13FO3S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, MgCl2, Tris HCl

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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: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.402→30.899 Å / Num. obs: 26664 / % possible obs: 92.8 % / Redundancy: 2.5 % / Rpim(I) all: 0.14 / Net I/σ(I): 172
Reflection shellResolution: 2.402→2.49 Å / Num. unique obs: 1321 / CC1/2: 0.561

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T1Z

5t1z


Resolution: 2.402→30.899 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 33.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 969 5.17 %
Rwork0.2231 17765 -
obs0.2254 18734 65.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126 Å2 / Biso mean: 43.9783 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.402→30.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3593 0 50 123 3766
Biso mean--37.75 40.85 -
Num. residues----463
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023758
X-RAY DIFFRACTIONf_angle_d0.4955089
X-RAY DIFFRACTIONf_chiral_restr0.019605
X-RAY DIFFRACTIONf_plane_restr0.002629
X-RAY DIFFRACTIONf_dihedral_angle_d12.6551355
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.42015-2.491230.3781380.292775920
2.5323-2.78690.31451600.2913299478
2.7869-3.18990.33121800.2649367294
3.1899-4.01750.2562080.2064370296
4.0175-100.21762220.1797365493
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)
10.36310.70160.10751.34310.21750.0309-0.13920.05780.3309-0.20750.13520.5561-0.2659-0.31030.16250.68840.6714-0.07360.36990.2990.4104-0.05669.8577-5.8677
25.5914-1.5552-0.92434.88910.26754.66430.0650.4133-0.2336-0.4644-0.0858-0.31270.15650.149-0.02050.2870.00660.10540.2336-0.02750.213320.1261-5.6311-2.8445
34.23882.0277-0.39163.32240.05932.85060.3113-0.11040.4377-0.285-0.3911-0.0008-0.6863-0.11450.08670.29150.02690.08740.2008-0.01780.25713.46344.22734.6712
43.65370.7218-1.31910.4716-1.09042.573-0.39850.4389-0.6152-0.3306-0.09140.37220.842-0.2180.41750.4643-0.02020.11760.2189-0.10930.360410.2085-15.6946-3.387
52.82830.18950.03161.02571.47722.219-0.1254-0.4812-0.89680.32210.05690.14941.19690.23850.06840.63160.0810.12840.1880.05360.359812.4554-17.97316.346
64.2889-0.9649-0.24930.5673-0.70971.86120.32360.16960.4639-0.3611-0.27190.2401-0.9754-0.6230.07430.37360.1662-0.00010.3404-0.01910.2165-0.40924.33313.815
74.9079-0.7231-1.78232.1690.25013.032-0.2738-0.2455-0.1650.07940.0114-0.24090.07390.24440.23340.25530.050.01510.18240.00420.128413.2178-4.894810.6214
80.5339-0.5241-0.01716.1772-1.0927.68090.2286-0.626-0.2394-0.29230.00951.2626-0.5692-1.9877-0.20530.27080.00990.08380.7713-0.12890.6503-17.2659-3.988725.9172
98.01323.34854.11875.28952.976.6289-1.2099-0.61210.0137-0.19990.5566-0.3804-0.6210.59260.50020.39210.09020.07570.4581-0.07120.30073.83791.137442.4559
104.99841.56021.18444.34532.96345.1494-0.8339-0.3606-0.56530.17840.3710.20710.61470.4417-0.13460.46620.01780.16530.27150.02630.32411.671-8.316934.7934
112.62510.4446-0.18351.4568-0.4272.6642-0.2649-0.1608-0.18610.0355-0.0291-0.07150.42040.23640.17680.33020.00610.10510.2019-0.01480.18693.3631-2.723429.136
124.44050.157-0.4522.05580.8115.7067-0.00730.02990.289-0.10840.2544-0.4763-1.0211.2529-0.25940.4401-0.13090.09380.4626-0.14170.336411.83638.574230.2413
134.69560.66041.24214.5334-0.21096.1307-0.04130.2819-0.1643-0.5098-0.0281-0.26630.0123-0.52110.06070.209-0.04640.03670.2555-0.03230.1882-4.1907-1.751622.099
143.4721-1.4001-0.68152.62450.26183.0771-0.2351-0.0197-0.1388-0.1249-0.01780.2575-0.2237-0.70790.11230.20910.0735-0.00590.2788-0.04150.1909-3.08120.548717.4833
151.88591.71123.0441.79711.97997.7213-0.8728-0.39830.07830.67490.0302-0.87510.21061.11720.38320.80990.374-0.01810.68280.1280.591915.1029-12.746433.5837
163.7512-0.85110.2161.86471.91285.19680.3989-0.59231.6964-0.0766-0.62280.0809-0.38761.03870.22870.5496-0.0910.30740.44170.00330.735524.766510.38431.343
170.7278-1.1912.11292.6287-3.62556.16710.2524-0.8768-1.22580.01190.1357-0.12590.9868-0.7967-0.12510.7442-0.22910.41520.35290.14530.70550.5961-19.878235.2492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 307 through 321 )A307 - 321
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 363 )A322 - 363
3X-RAY DIFFRACTION3chain 'A' and (resid 364 through 394 )A364 - 394
4X-RAY DIFFRACTION4chain 'A' and (resid 395 through 407 )A395 - 407
5X-RAY DIFFRACTION5chain 'A' and (resid 408 through 437 )A408 - 437
6X-RAY DIFFRACTION6chain 'A' and (resid 438 through 496 )A438 - 496
7X-RAY DIFFRACTION7chain 'A' and (resid 497 through 548 )A497 - 548
8X-RAY DIFFRACTION8chain 'B' and (resid 307 through 321 )B307 - 321
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 338 )B322 - 338
10X-RAY DIFFRACTION10chain 'B' and (resid 339 through 371 )B339 - 371
11X-RAY DIFFRACTION11chain 'B' and (resid 372 through 405 )B372 - 405
12X-RAY DIFFRACTION12chain 'B' and (resid 406 through 437 )B406 - 437
13X-RAY DIFFRACTION13chain 'B' and (resid 438 through 472 )B438 - 472
14X-RAY DIFFRACTION14chain 'B' and (resid 473 through 527 )B473 - 527
15X-RAY DIFFRACTION15chain 'B' and (resid 528 through 548 )B528 - 548
16X-RAY DIFFRACTION16chain 'C' and (resid 180 through 187 )C180 - 187
17X-RAY DIFFRACTION17chain 'D' and (resid 28 through 35 )D28 - 35

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