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Yorodumi- PDB-4pps: Crystal Structure of the Estrogen Receptor alpha Ligand-binding D... -
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-Basic information
Entry | Database: PDB / ID: 4pps | ||||||
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Title | Crystal Structure of the Estrogen Receptor alpha Ligand-binding Domain in Complex with an A-CD ring estrogen derivative | ||||||
Components |
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Keywords | PROTEIN BINDING / nuclear hormone receptor / transcription factor / ligand-binding / nucleus | ||||||
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 / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 ...regulation of epithelial cell apoptotic process / antral ovarian follicle growth / G protein-coupled estrogen receptor activity / regulation of branching involved in prostate gland morphogenesis / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / 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 / locomotor rhythm / mammary gland branching involved in pregnancy / negative regulation of smooth muscle cell apoptotic process / uterus development / vagina development / aryl hydrocarbon receptor binding / TFIIB-class transcription factor binding / androgen metabolic process / regulation of lipid metabolic process / steroid hormone receptor signaling pathway / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / mammary gland alveolus development / 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 receptor-mediated steroid hormone signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Nuclear signaling by ERBB4 / RNA polymerase II preinitiation complex assembly / Recycling of bile acids and salts / cellular response to hormone stimulus / 14-3-3 protein binding / protein localization to chromatin / estrogen receptor signaling pathway / positive regulation of adipose tissue development / RORA activates gene expression / peroxisome proliferator activated receptor signaling pathway / steroid binding / nitric-oxide synthase regulator activity / Regulation of lipid metabolism by PPARalpha / TBP-class protein binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of cellular response to insulin stimulus / ESR-mediated signaling / BMAL1:CLOCK,NPAS2 activates circadian gene expression / transcription corepressor binding / negative regulation of miRNA transcription / Activation of gene expression by SREBF (SREBP) / SUMOylation of transcription cofactors / nuclear receptor coactivator activity / positive regulation of nitric-oxide synthase activity / cellular response to estradiol stimulus / transcription coregulator binding / response to progesterone / nuclear receptor binding / stem cell differentiation / nuclear estrogen receptor binding / positive regulation of DNA-binding transcription factor activity / circadian regulation of gene expression / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / euchromatin / negative regulation of DNA-binding transcription factor activity / PPARA activates gene expression / Cytoprotection by HMOX1 / transcription coactivator binding / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / beta-catenin binding / response to estrogen / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Regulation of RUNX2 expression and activity / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / positive regulation of nitric oxide biosynthetic process / Ovarian tumor domain proteases / Circadian Clock / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / ATPase binding / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / regulation of inflammatory response / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / fibroblast proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.929 Å | ||||||
Authors | Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. ...Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W. | ||||||
Citation | Journal: Elife / Year: 2014 Title: Resveratrol modulates the inflammatory response via an estrogen receptor-signal integration network. Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / ...Authors: Nwachukwu, J.C. / Srinivasan, S. / Bruno, N.E. / Parent, A.A. / Hughes, T.S. / Pollock, J.A. / Gjyshi, O. / Cavett, V. / Nowak, J. / Garcia-Ordonez, R.D. / Houtman, R. / Griffin, P.R. / Kojetin, D.J. / Katzenellenbogen, J.A. / Conkright, M.D. / Nettles, K.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pps.cif.gz | 219.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pps.ent.gz | 176.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pps.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pps_validation.pdf.gz | 468.4 KB | Display | wwPDB validaton report |
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Full document | 4pps_full_validation.pdf.gz | 474.6 KB | Display | |
Data in XML | 4pps_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 4pps_validation.cif.gz | 33.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pp/4pps ftp://data.pdbj.org/pub/pdb/validation_reports/pp/4pps | HTTPS FTP |
-Related structure data
Related structure data | 4pp6C 4pppC 2qa8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 27832.783 Da / Num. of mol.: 2 / Fragment: ligand-binding domain (UNP residues 305-548) / Mutation: Y537S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR, ESR1, NR3A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03372 #2: Protein/peptide | Mass: 1450.686 Da / Num. of mol.: 2 Fragment: receptor-interacting peptide (UNP residues 687-698) Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596 #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.05 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.3 Details: 15% PEG3350, 0.05 M magnesium chloride, 0.067 M sodium chloride, 0.1 M Tris, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2010 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.929→33.541 Å / Num. all: 38369 / Num. obs: 38369 / % possible obs: 98.68 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 27.7 |
Reflection shell | Resolution: 1.929→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3443 / % possible all: 89.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QA8 Resolution: 1.929→33.541 Å / SU ML: 0.41 / σ(F): 0 / Phase error: 21.7 / 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: 38.511 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.929→33.541 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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