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Yorodumi- PDB-4tuz: Crystal structure of hERa-LBD (Y537S) in complex with alpha-zearalenol -
+Open data
-Basic information
Entry | Database: PDB / ID: 4tuz | |||||||||
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Title | Crystal structure of hERa-LBD (Y537S) in complex with alpha-zearalenol | |||||||||
Components |
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Keywords | NUCLEAR PROTEIN / nuclear hormone receptor ligand binding domain endocrine disruptor environmental compound | |||||||||
Function / homology | Function and homology information labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / hypothalamus development / regulation of branching involved in prostate gland morphogenesis / male mating behavior ...labyrinthine layer morphogenesis / regulation of thyroid hormone mediated signaling pathway / positive regulation of transcription from RNA polymerase II promoter by galactose / positive regulation of female receptivity / regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / hypothalamus development / regulation of branching involved in prostate gland morphogenesis / male mating behavior / RUNX1 regulates transcription of genes involved in WNT signaling / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / estrous cycle / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / mammary gland alveolus development / intracellular estrogen receptor signaling pathway / 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 / positive regulation of phospholipase C activity / nuclear retinoid X receptor binding / intracellular steroid hormone receptor signaling pathway / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / histone acetyltransferase activity / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / protein localization to chromatin / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / lactation / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / steroid binding / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / nitric-oxide synthase regulator activity / cerebellum development / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / 14-3-3 protein binding / transcription corepressor binding / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / negative regulation of miRNA transcription / nuclear receptor coactivator activity / response to progesterone / cellular response to estradiol stimulus / transcription coregulator binding / nuclear estrogen receptor binding / stem cell differentiation / positive regulation of nitric-oxide synthase activity / nuclear receptor binding / hippocampus development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / euchromatin / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / transcription coactivator binding / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / beta-catenin binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Delfosse, V. / Grimaldi, M. / Bourguet, W. | |||||||||
Funding support | France, 1items
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Citation | Journal: Acta Pharmacol. Sin. / Year: 2015 Title: A structural perspective on nuclear receptors as targets of environmental compounds. Authors: Delfosse, V. / Maire, A.L. / Balaguer, P. / Bourguet, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4tuz.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4tuz.ent.gz | 93.6 KB | Display | PDB format |
PDBx/mmJSON format | 4tuz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/4tuz ftp://data.pdbj.org/pub/pdb/validation_reports/tu/4tuz | HTTPS FTP |
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-Related structure data
Related structure data | 4tv1C 3uudS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 29070.217 Da / Num. of mol.: 1 / Fragment: Residues 302-552 / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / References: UniProt: P03372 |
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#2: Protein | Mass: 29086.217 Da / Num. of mol.: 1 / Fragment: Residues 302-552 / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR1, ESR, NR3A1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P03372 |
-Protein/peptide , 1 types, 2 molecules FG
#3: Protein/peptide | Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: Residues 686-698 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788*PLUS, histone acetyltransferase |
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-Non-polymers , 4 types, 273 molecules
#4: Chemical | #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.98 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 / Details: 300-340 mM NaCl 100 mM Hepes 24-32 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97934 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→46.52 Å / Num. obs: 40075 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rsym value: 0.05 / Net I/σ(I): 13.85 |
Reflection shell | Resolution: 1.9→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.68 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UUD Resolution: 1.9→46.52 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.614 Å2 / ksol: 0.361 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→46.52 Å
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Refine LS restraints |
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LS refinement shell |
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