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- PDB-1sj0: Human Estrogen Receptor Alpha Ligand-binding Domain in Complex wi... -

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Basic information

Entry
Database: PDB / ID: 1sj0
TitleHuman Estrogen Receptor Alpha Ligand-binding Domain in Complex with the Antagonist Ligand 4-D
ComponentsEstrogen receptor
KeywordsHORMONE/GROWTH FACTOR RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ER-ALPHA / ANTAGONIST / HORMONE-GROWTH FACTOR RECEPTOR COMPLEX
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 mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / 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 / 14-3-3 protein binding / TBP-class protein binding / steroid binding / nitric-oxide synthase regulator activity / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / 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 / 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 / positive regulation of nitric oxide biosynthetic process / male gonad development / positive regulation of fibroblast proliferation / sequence-specific double-stranded DNA binding / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / 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 / chromatin / regulation of DNA-templated transcription / 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 / 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-E4D / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.9 Å
AuthorsKim, S. / Wu, J.Y. / Birzin, E.T. / Chan, W. / Pai, L.Y. / Yang, Y.T. / Mosley, R.T. / Fitzgerald, P.M. / Sharma, N. / DiNinno, F. ...Kim, S. / Wu, J.Y. / Birzin, E.T. / Chan, W. / Pai, L.Y. / Yang, Y.T. / Mosley, R.T. / Fitzgerald, P.M. / Sharma, N. / DiNinno, F. / Rohrer, S.P. / Schaeffer, J.M. / Hammond, M.L.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Estrogen Receptor Ligands. II. Discovery of Benzoxathiins as Potent, Selective Estrogen Receptor alpha Modulators.
Authors: Kim, S. / Wu, J.Y. / Birzin, E.T. / Frisch, K. / Chan, W. / Pai, L.Y. / Yang, Y.T. / Mosley, R.T. / Fitzgerald, P.M. / Sharma, N. / Dahllund, J. / Thorsell, A.G. / DiNinno, F. / Rohrer, S.P. ...Authors: Kim, S. / Wu, J.Y. / Birzin, E.T. / Frisch, K. / Chan, W. / Pai, L.Y. / Yang, Y.T. / Mosley, R.T. / Fitzgerald, P.M. / Sharma, N. / Dahllund, J. / Thorsell, A.G. / DiNinno, F. / Rohrer, S.P. / Schaeffer, J.M. / Hammond, M.L.
History
DepositionMar 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7802
Polymers28,3161
Non-polymers4641
Water2,738152
1
A: Estrogen receptor
hetero molecules

A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5604
Polymers56,6332
Non-polymers9272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area5050 Å2
ΔGint-27 kcal/mol
Surface area22090 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.480, 58.480, 276.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-1001-

HOH

21A-1002-

HOH

31A-1049-

HOH

41A-1099-

HOH

51A-1102-

HOH

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Components

#1: Protein Estrogen receptor / / ER / Estradiol receptor / ER-alpha


Mass: 28316.324 Da / Num. of mol.: 1 / Fragment: Ligand Binding Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, NR3A1, ESR / Production host: Escherichia coli (E. coli) / References: UniProt: P03372
#2: Chemical ChemComp-E4D / (2S,3R)-2-(4-(2-(PIPERIDIN-1-YL)ETHOXY)PHENYL)-2,3-DIHYDRO-3-(4-HYDROXYPHENYL)BENZO[B][1,4]OXATHIIN-6-OL / COMPOUND 4-D


Mass: 463.588 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H29NO4S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.1
Details: 2-10% PEG 3350, 0.02-0.20 MMGCL2, PH 7.1 Imidazole , VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→99.9 Å / Num. obs: 19370 / % possible obs: 82.8 % / Observed criterion σ(I): 1 / Redundancy: 6.228 % / Biso Wilson estimate: 46.9 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 39.983
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 2.32 % / Rmerge(I) obs: 0.3558 / Mean I/σ(I) obs: 3.042 / Rsym value: 0.3558 / % possible all: 54.1

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
SHELXL97-1refinement
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.9→10 Å / Num. parameters: 8469 / Num. restraintsaints: 8090 / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 950 5 %random
Rwork0.218 ---
obs0.218 18187 82.8 %-
all-18187 --
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2217
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1934 0 33 152 2119
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.246
X-RAY DIFFRACTIONs_zero_chiral_vol0.023
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.007
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.092

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