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- PDB-2i0j: Benzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs... -

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Basic information

Entry
Database: PDB / ID: 2i0j
TitleBenzopyrans are Selective Estrogen Receptor beta Agonists (SERBAs) with Novel Activity in Models of Benign Prostatic Hyperplasia
ComponentsEstrogen receptor alpha
KeywordsTRANSCRIPTION / Nuclear receptor ligand binding domain
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 receptor signaling pathway / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / : / 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 / protein localization to chromatin / 14-3-3 protein binding / TBP-class protein binding / nitric-oxide synthase regulator activity / steroid binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / transcription corepressor binding / negative regulation of miRNA transcription / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / stem cell differentiation / nuclear estrogen receptor binding / 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 / male gonad development / positive regulation of nitric oxide biosynthetic process / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / PIP3 activates AKT signaling / response to estradiol / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / ATPase binding / 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 / regulation of DNA-templated transcription / chromatin / 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 / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
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-I0G / Estrogen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, Y.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Benzopyrans are selective estrogen receptor Beta agonists with novel activity in models of benign prostatic hyperplasia.
Authors: Norman, B.H. / Dodge, J.A. / Richardson, T.I. / Borromeo, P.S. / Lugar, C.W. / Jones, S.A. / Chen, K. / Wang, Y. / Durst, G.L. / Barr, R.J. / Montrose-Rafizadeh, C. / Osborne, H.E. / Amos, R. ...Authors: Norman, B.H. / Dodge, J.A. / Richardson, T.I. / Borromeo, P.S. / Lugar, C.W. / Jones, S.A. / Chen, K. / Wang, Y. / Durst, G.L. / Barr, R.J. / Montrose-Rafizadeh, C. / Osborne, H.E. / Amos, R.M. / Guo, S. / Boodhoo, A. / Krishnan, V.
History
DepositionAug 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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

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Assembly

Deposited unit
A: Estrogen receptor alpha
B: Estrogen receptor alpha
C: Estrogen receptor alpha
D: Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,4008
Polymers111,2704
Non-polymers1,1294
Water00
1
A: Estrogen receptor alpha
B: Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2004
Polymers55,6352
Non-polymers5652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-3 kcal/mol
Surface area19720 Å2
MethodPISA
2
C: Estrogen receptor alpha
D: Estrogen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2004
Polymers55,6352
Non-polymers5652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-2 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.503, 173.144, 58.522
Angle α, β, γ (deg.)90.000, 119.480, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains two biological units. One biological unit consists of chains A and B, the other C and D.

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Components

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


Mass: 27817.594 Da / Num. of mol.: 4 / Fragment: steroid binding domain / Mutation: C381S, C417S, C530S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET19 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03372
#2: Chemical
ChemComp-I0G / (3AS,4R,9BR)-4-(4-HYDROXYPHENYL)-1,2,3,3A,4,9B-HEXAHYDROCYCLOPENTA[C]CHROMEN-8-OL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18O3 / Comment: agonist*YM

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris, 0.2M magnesium chloride, 20% PEG 4000, 10% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 9, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 22417 / Num. obs: 20086 / % possible obs: 89.6 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.12 / Χ2: 1.149 / Net I/σ(I): 6
Reflection shellResolution: 2.8→3.02 Å / Rmerge(I) obs: 0.355 / Num. unique all: 1450 / Χ2: 0.819 / % possible all: 57.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
AMoREphasing
CNX2002refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1A52

1a52


Resolution: 2.9→27.72 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1319503.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1039 5.2 %RANDOM
Rwork0.241 ---
all0.242 20086 --
obs0.242 20086 89.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.532 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 59 Å2
Baniso -1Baniso -2Baniso -3
1-13.74 Å20 Å221.16 Å2
2---21.03 Å20 Å2
3---7.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.9→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7134 0 84 0 7218
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.292
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.742.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 115 4.9 %
Rwork0.377 2222 -
obs-2337 62.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2lig.parlig.top
X-RAY DIFFRACTION3water_rep.paramwater_rep.top

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