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- PDB-4mg5: Crystal structure of hERa-LBD (Y537S) in complex with chlordecone -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mg5 | |||||||||
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Title | Crystal structure of hERa-LBD (Y537S) in complex with chlordecone | |||||||||
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![]() | HORMONE RECEPTOR / ligand-binding domain of nuclear hormone receptor | |||||||||
Function / homology | ![]() 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 | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Delfosse, V. / Grimaldi, M. / Bourguet, W. | |||||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 144.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 21.4 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4mg6C ![]() 4mg7C ![]() 4mg8C ![]() 4mg9C ![]() 4mgaC ![]() 4mgbC ![]() 4mgcC ![]() 4mgdC ![]() 3uudS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29070.217 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.) ![]() ![]() ![]() #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.) ![]() #3: Chemical | #4: Chemical | Mass: 508.652 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H2Cl10O2 / Feature type: SUBJECT OF INVESTIGATION #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.75 Details: 340 mM sodium chloride, 100 mM HEPES, 32% PEG3350, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011 |
Radiation | Monochromator: liquid nitrogen cooled channel-cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→46.36 Å / Num. obs: 30297 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.35 Å2 / Rsym value: 0.065 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 2.05→2.17 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.48 / Num. unique obs: 4761 / Rsym value: 0.48 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3UUD Resolution: 2.05→46.36 Å / SU ML: 0.2318 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 25.078 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.97 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→46.36 Å
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Refine LS restraints |
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LS refinement shell |
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