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- PDB-2iog: Human estrogen receptor alpha ligand-binding domain in complex wi... -

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Basic information

Entry
Database: PDB / ID: 2iog
TitleHuman estrogen receptor alpha ligand-binding domain in complex with compound 11F
ComponentsEstrogen receptor
KeywordsHORMONE / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ER-ALPHA / ANTAGONIST
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 / 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 / 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 / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / epithelial cell proliferation involved in mammary gland duct elongation / prostate epithelial cord elongation / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / TFIIB-class transcription factor binding / steroid hormone receptor signaling pathway / 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 / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / positive regulation of DNA-binding transcription factor activity / 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 DNA-binding transcription factor activity / negative regulation of miRNA transcription / nitric-oxide synthase regulator activity / ESR-mediated signaling / TBP-class protein binding / transcription coregulator binding / nuclear estrogen receptor binding / transcription corepressor binding / stem cell differentiation / cellular response to estradiol stimulus / SUMOylation of intracellular receptors / euchromatin / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / Regulation of RUNX2 expression and activity / transcription coactivator binding / nuclear receptor activity / Ovarian tumor domain proteases / positive regulation of fibroblast proliferation / male gonad development / 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 / DNA-binding transcription activator activity, RNA polymerase II-specific / 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 transcription by RNA polymerase II / regulation of DNA-templated transcription / 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-IOG / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 1.6 Å
AuthorsFitzgerald, P.M.D. / Sharma, N.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Estrogen receptor ligands. Part 16: 2-Aryl indoles as highly subtype selective ligands for ERalpha
Authors: Dykstra, K.D. / Guo, L. / Birzin, E.T. / Chan, W. / Yang, Y.T. / Hayes, E.C. / DaSilva, C.A. / Pai, L.-Y. / Mosley, R.T. / Kraker, B. / Fitzgerald, P.M.D. / DiNinno, F. / Rohrer, S.P. / ...Authors: Dykstra, K.D. / Guo, L. / Birzin, E.T. / Chan, W. / Yang, Y.T. / Hayes, E.C. / DaSilva, C.A. / Pai, L.-Y. / Mosley, R.T. / Kraker, B. / Fitzgerald, P.M.D. / DiNinno, F. / Rohrer, S.P. / Schaeffer, J.M. / Hammond, M.L.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 7, 2021Group: Derived calculations / Refinement description / Category: refine / struct_site
Item: _refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id ..._refine.ls_percent_reflns_obs / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jul 28, 2021Group: Refinement description / Category: refine / Item: _refine.ls_percent_reflns_obs
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6582
Polymers28,1321
Non-polymers5261
Water3,315184
1
A: Estrogen receptor
hetero molecules

A: Estrogen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3164
Polymers56,2642
Non-polymers1,0512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.220, 58.220, 276.660
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-607-

HOH

21A-634-

HOH

31A-736-

HOH

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Components

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


Mass: 28132.088 Da / Num. of mol.: 1 / Fragment: Steroid-binding region, residues 306-554
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-IOG / N-[(1R)-3-(4-HYDROXYPHENYL)-1-METHYLPROPYL]-2-[2-PHENYL-6-(2-PIPERIDIN-1-YLETHOXY)-1H-INDOL-3-YL]ACETAMIDE


Mass: 525.681 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H39N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
Crystal growTemperature: 297 K / pH: 7.1
Details: 2-10% PEG 3350, 0.02-0.20M MGCL2, IMIDAZOLE, VAPOR DIFFUSION, HANGING DROP, PH 7.10, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Sep 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→99.9 Å / Num. obs: 68081 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 13.28 % / Rmerge(I) obs: 0.1171 / Rsym value: 0.1171 / Net I/σ(I): 32.053
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 7.37 % / Rmerge(I) obs: 0.8691 / Mean I/σ(I) obs: 2.722 / Rsym value: 0.8691 / % possible all: 89.4

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Processing

Software
NameVersionClassification
SHELXL97-1refinement
ADSCQuantumdata collection
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT / Resolution: 1.6→10 Å / Num. parameters: 19440 / Num. restraintsaints: 23880 / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.328 376 5 %RANDOM
obs0.212 -97.7 %-
all-36605 --
Solvent computationSolvent model: SHELXL TWO-PARAMETER (SWAT)
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2159.5
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1938 0 39 184 2161
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.319
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.039
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.063
X-RAY DIFFRACTIONs_approx_iso_adps0.07

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