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Yorodumi- PDB-4mgc: Crystal structure of hERa-LBD (Y537S) in complex with benzophenone-2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mgc | ||||||
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Title | Crystal structure of hERa-LBD (Y537S) in complex with benzophenone-2 | ||||||
Components |
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Keywords | HORMONE RECEPTOR / ligand-binding domain of nuclear hormone receptor | ||||||
Function / homology | Function and homology information 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 / regulation of epithelial cell apoptotic process / hypothalamus development / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / male mating behavior ...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 / regulation of epithelial cell apoptotic process / hypothalamus development / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / 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 / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / mammary gland alveolus development / estrogen receptor signaling pathway / cellular response to estrogen stimulus / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / estrogen response element binding / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / : / nuclear retinoid X receptor binding / nuclear receptor-mediated steroid hormone signaling pathway / response to retinoic acid / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / histone acetyltransferase / cellular response to hormone stimulus / protein localization to chromatin / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / 14-3-3 protein binding / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / lactation / positive regulation of neuron differentiation / nitric-oxide synthase regulator activity / steroid binding / Regulation of lipid metabolism by PPARalpha / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / ESR-mediated signaling / cerebellum development / transcription corepressor binding / BMAL1:CLOCK,NPAS2 activates circadian gene expression / negative regulation of miRNA transcription / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / stem cell differentiation / hippocampus development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / SUMOylation of intracellular receptors / euchromatin / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / beta-catenin binding / transcription coactivator binding / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / response to estrogen / RNA polymerase II transcription regulator complex / 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 Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Delfosse, V. / Grimaldi, M. / Bourguet, W. | ||||||
Citation | Journal: Environ.Health Perspect. / Year: 2014 Title: Structural and functional profiling of environmental ligands for estrogen receptors. Authors: Delfosse, V. / Grimaldi, M. / Cavailles, V. / 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 | 4mgc.cif.gz | 116.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mgc.ent.gz | 89.2 KB | Display | PDB format |
PDBx/mmJSON format | 4mgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mgc_validation.pdf.gz | 475.8 KB | Display | wwPDB validaton report |
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Full document | 4mgc_full_validation.pdf.gz | 481 KB | Display | |
Data in XML | 4mgc_validation.xml.gz | 22 KB | Display | |
Data in CIF | 4mgc_validation.cif.gz | 30.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mg/4mgc ftp://data.pdbj.org/pub/pdb/validation_reports/mg/4mgc | HTTPS FTP |
-Related structure data
Related structure data | 4mg5C 4mg6C 4mg7C 4mg8C 4mg9C 4mgaC 4mgbC 4mgdC 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
#1: Protein | Mass: 29086.217 Da / Num. of mol.: 2 / Fragment: ligand binding domain (UNP residues 302-552) / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03372 #2: Protein/peptide | Mass: 1591.880 Da / Num. of mol.: 2 / Fragment: coactivator peptide SRC-1 (UNP residues 686-698) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788 #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.11 Å3/Da / Density % sol: 41.82 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 300 mM sodium chloride, 100 mM HEPES, 28% PEG3350, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 10, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→46.12 Å / Num. obs: 27695 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 0.072 / Net I/σ(I): 15.41 |
Reflection shell | Resolution: 2.15→2.28 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.66 / Rsym value: 0.448 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3UUD Resolution: 2.15→46.119 Å / SU ML: 0.29 / σ(F): 2 / Phase error: 22.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.863 Å2 / ksol: 0.362 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.15→46.119 Å
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Refine LS restraints |
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LS refinement shell |
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