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Yorodumi- PDB-2j7x: STRUCTURE OF ESTRADIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLE... -
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-Basic information
Entry | Database: PDB / ID: 2j7x | ||||||
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Title | STRUCTURE OF ESTRADIOL-BOUND ESTROGEN RECEPTOR BETA LBD IN COMPLEX WITH LXXLL MOTIF FROM NCOA5 | ||||||
Components |
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Keywords | TRANSCRIPTION / ZINC-FINGER / NUCLEAR RECEPTOR / PHOSPHORYLATION / STEROID-BINDING / GLYCOPROTEIN / TRANSCRIPTION REGULATION | ||||||
Function / homology | Function and homology information negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / epithelial cell maturation involved in prostate gland development / amygdala development ...negative regulation of behavior / cellular response to magnetism / response to bisphenol A / ESR-mediated signaling / PIP3 activates AKT signaling / estrogen binding / estradiol binding / response to insecticide / epithelial cell maturation involved in prostate gland development / amygdala development / response to human chorionic gonadotropin / hormone-mediated apoptotic signaling pathway / Extra-nuclear estrogen signaling / Sertoli cell proliferation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / prostate gland development / Sertoli cell development / response to genistein / Nuclear Receptor transcription pathway / organic cyclic compound binding / hormone binding / negative regulation of androgen receptor signaling pathway / steroid hormone binding / response to salt / prostate gland epithelium morphogenesis / peroxisome proliferator activated receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / nuclear steroid receptor activity / hypothalamus development / negative regulation of feeding behavior / female gonad development / response to testosterone / heterocyclic compound binding / nuclear estrogen receptor activity / response to dexamethasone / androgen receptor signaling pathway / uterus development / vagina development / cellular response to organic cyclic compound / estrous cycle / negative regulation of reactive oxygen species metabolic process / regulation of signal transduction / behavioral fear response / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / ovarian follicle development / negative regulation of insulin receptor signaling pathway / steroid binding / response to nutrient levels / cerebellum development / response to hormone / epithelial cell proliferation / response to activity / cellular response to estradiol stimulus / promoter-specific chromatin binding / protein-DNA complex / negative regulation of smooth muscle cell proliferation / neuron migration / brain development / response to organic cyclic compound / positive regulation of DNA-binding transcription factor activity / response to estrogen / vasodilation / transcription corepressor activity / negative regulation of epithelial cell proliferation / nuclear receptor activity / male gonad development / actin cytoskeleton / cellular response to xenobiotic stimulus / insulin receptor signaling pathway / response to estradiol / glucose homeostasis / regulation of cell population proliferation / cellular response to lipopolysaccharide / DNA-binding transcription activator activity, RNA polymerase II-specific / perikaryon / response to ethanol / negative regulation of neuron apoptotic process / sequence-specific DNA binding / cell population proliferation / positive regulation of ERK1 and ERK2 cascade / learning or memory / response to xenobiotic stimulus / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / neuronal cell body / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Walton, J. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M. | ||||||
Citation | Journal: To be Published Title: Structure of Agonist-Bound Estrogen Receptor Beta Lbd in Complex with Lxxll Motif from Ncoa5 Authors: Pike, A.C.W. / Brzozowski, A.M. / Hubbard, R.E. / Walton, J. / Bonn, T. / Thorsell, A.-G. / Engstrom, O. / Ljunggren, J. / Gustaffson, J.-A. / Carlquist, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2j7x.cif.gz | 64.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2j7x.ent.gz | 47.1 KB | Display | PDB format |
PDBx/mmJSON format | 2j7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7x ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7x | HTTPS FTP |
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-Related structure data
Related structure data | 2j7yC 1qknS 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 on special symmetry positions |
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-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 28686.002 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, RESIDUES 255-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): GI724 / References: UniProt: Q62986 |
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#2: Protein/peptide | Mass: 1937.204 Da / Num. of mol.: 1 / Fragment: LXXLL PEPTIDE, RESIDUES 338-354 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9HCD5 |
-Non-polymers , 5 types, 105 molecules
#3: Chemical | ChemComp-EST / | ||||||
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#4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-SO4 / | #6: Chemical | ChemComp-BCT / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55 % |
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Crystal grow | pH: 8 Details: 5-7% PEG 8K, 5-7% PEG 1K, 0.13M LITHIUM SULPHATE, 0.1M TRIS PH 8.0 . |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→40 Å / Num. obs: 20776 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 15 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QKN Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.751 / SU ML: 0.096 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.55 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→40 Å
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