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Yorodumi- PDB-7xvy: Human Estrogen Receptor beta Ligand-binding Domain in Complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xvy | ||||||
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Title | Human Estrogen Receptor beta Ligand-binding Domain in Complex with S-DPN | ||||||
Components |
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Keywords | TRANSCRIPTION/INHIBITOR / Inhibitor / TRANSCRIPTION / TRANSCRIPTION-INHIBITOR complex | ||||||
Function / homology | Function and homology information receptor antagonist activity / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity ...receptor antagonist activity / labyrinthine layer morphogenesis / regulation of thyroid hormone receptor signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / estrous cycle / cellular response to estrogen stimulus / estrogen response element binding / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / progesterone receptor signaling pathway / nuclear retinoid X receptor binding / response to retinoic acid / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / positive regulation of neuron differentiation / lactation / Regulation of lipid metabolism by PPARalpha / regulation of cellular response to insulin stimulus / ESR-mediated signaling / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / cellular response to estradiol stimulus / hippocampus development / response to progesterone / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of DNA-binding transcription factor activity / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / negative regulation of cell growth / cerebral cortex development / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / male gonad development / nuclear receptor activity / Circadian Clock / PIP3 activates AKT signaling / cell-cell signaling / response to estradiol / HATs acetylate histones / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.544 Å | ||||||
Authors | Furuya, N. / Handa, C. | ||||||
Funding support | 1items
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Citation | Journal: J.Steroid Biochem.Mol.Biol. / Year: 2022 Title: Evaluating the correlation of binding affinities between isothermal titration calorimetry and fragment molecular orbital method of estrogen receptor beta with diarylpropionitrile (DPN) or DPN derivatives. Authors: Handa, C. / Yamazaki, Y. / Yonekubo, S. / Furuya, N. / Momose, T. / Ozawa, T. / Furuishi, T. / Fukuzawa, K. / Yonemochi, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xvy.cif.gz | 199 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xvy.ent.gz | 153.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xvy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7xvy_validation.pdf.gz | 902.2 KB | Display | wwPDB validaton report |
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Full document | 7xvy_full_validation.pdf.gz | 908.6 KB | Display | |
Data in XML | 7xvy_validation.xml.gz | 21.6 KB | Display | |
Data in CIF | 7xvy_validation.cif.gz | 31.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xv/7xvy ftp://data.pdbj.org/pub/pdb/validation_reports/xv/7xvy | HTTPS FTP |
-Related structure data
Related structure data | 7xvzC 7xwpC 7xwqC 7xwrC 2giuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27702.578 Da / Num. of mol.: 2 / Fragment: ligand-binding domain / Mutation: C334S, C369S, C481S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Plasmid: pGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92731 #2: Protein/peptide | Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.02 Å3/Da / Density % sol: 39.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 16-20% PEG3350, 100 mM BisTris pH6.5, 200 mM Magnesium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 13, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→46.443 Å / Num. obs: 69739 / % possible obs: 99.6 % / Redundancy: 11.6 % / CC1/2: 0.998 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 1.54→1.57 Å / Num. unique obs: 511 / CC1/2: 0.577 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2giu Resolution: 1.544→46.443 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.212 / SU B: 1.563 / SU ML: 0.057 / Average fsc free: 0.9629 / Average fsc work: 0.9724 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.091 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.881 Å2
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Refinement step | Cycle: LAST / Resolution: 1.544→46.443 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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