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Yorodumi- PDB-2qe4: Estrogen receptor alpha ligand-binding domain in complex with a b... -
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-Basic information
Entry | Database: PDB / ID: 2qe4 | ||||||
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Title | Estrogen receptor alpha ligand-binding domain in complex with a benzopyran agonist | ||||||
Components | Estrogen receptor | ||||||
Keywords | TRANSCRIPTION / nuclear receptor / ligand-binding domain / Alternative splicing / DNA-binding / Lipid-binding / Metal-binding / Nuclear protein / Phosphorylation / Polymorphism / Steroid-binding / Transcription regulation / Zinc / Zinc-finger | ||||||
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 / prostate epithelial cord elongation / epithelial cell development / negative regulation of smooth muscle cell apoptotic process / mammary gland branching involved in pregnancy / uterus development / vagina development / androgen metabolic process / TFIIB-class transcription factor binding / steroid hormone mediated signaling pathway / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / positive regulation of phospholipase C activity / 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 / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / nitric-oxide synthase regulator activity / ESR-mediated signaling / 14-3-3 protein binding / 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 / euchromatin / SUMOylation of intracellular receptors / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / beta-catenin binding / Nuclear Receptor transcription pathway / response to estrogen / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / Regulation of RUNX2 expression and activity / nuclear receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of DNA-binding transcription factor activity / positive regulation of fibroblast proliferation / Ovarian tumor domain proteases / sequence-specific double-stranded DNA binding / response to estradiol / PIP3 activates AKT signaling / phospholipase C-activating G protein-coupled receptor signaling pathway / ATPase binding / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / regulation of inflammatory response / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Norman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S.Q. ...Norman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S.Q. / Reilly, J.E. / Ryter, K.T. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2007 Title: Benzopyrans as selective estrogen receptor beta agonists (SERBAs). Part 4: Functionalization of the benzopyran A-ring. Authors: Norman, B.H. / Richardson, T.I. / Dodge, J.A. / Pfeifer, L.A. / Durst, G.L. / Wang, Y. / Durbin, J.D. / Krishnan, V. / Dinn, S.R. / Liu, S. / Reilly, J.E. / Ryter, K.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qe4.cif.gz | 94.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qe4.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 2qe4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/2qe4 ftp://data.pdbj.org/pub/pdb/validation_reports/qe/2qe4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The ASU forms a biological assembly (dimer). |
-Components
#1: Protein | Mass: 28297.172 Da / Num. of mol.: 2 / Fragment: Ligand binding domain / Mutation: C381S, C417S, C530S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03372 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.13 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 100 mM MES pH 6.8, 0.5 M MgCl2, 15% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 10, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→47.98 Å / Num. all: 18414 / Num. obs: 17217 / % possible obs: 93.5 % / Observed criterion σ(I): 2.54 / Redundancy: 2.7 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2.55 / Num. unique all: 1813 / % possible all: 80.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→47.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1689182.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7202 Å2 / ksol: 0.38013 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→47.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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