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Yorodumi- PDB-1x76: CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-697 -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x76 | ||||||
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Title | CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH WAY-697 | ||||||
Components |
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Keywords | TRANSCRIPTION / ESTROGEN RECEPTOR / ESTROGEN RECEPTOR BETA / ER-BETA / ER / ESTROGEN / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / AGONIST | ||||||
Function / homology | Function and homology information receptor antagonist activity / 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 / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity ...receptor antagonist activity / 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 / nuclear steroid receptor activity / hypothalamus development / male mating behavior / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / nuclear estrogen receptor activity / cellular response to Thyroglobulin triiodothyronine / estrous cycle / Synthesis of bile acids and bile salts / 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 / response to retinoic acid / 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 / positive regulation of adipose tissue development / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / lactation / positive regulation of neuron differentiation / Regulation of lipid metabolism by PPARalpha / steroid binding / ESR-mediated signaling / cerebellum development / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity / cellular response to estradiol stimulus / response to progesterone / hippocampus development / nuclear receptor binding / nuclear estrogen receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / negative regulation of cell growth / Cytoprotection by HMOX1 / cerebral cortex development / positive regulation of DNA-binding transcription factor activity / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / RNA polymerase II transcription regulator complex / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / male gonad development / Circadian Clock / cell-cell signaling / PIP3 activates AKT signaling / response to estradiol / HATs acetylate histones / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Estrogen-dependent gene expression / transcription regulator complex / Extra-nuclear estrogen signaling / transcription coactivator activity / protein dimerization activity / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / intracellular membrane-bounded organelle / chromatin binding / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. ...Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2004 Title: Structure-Based Design of Estrogen Receptor-Beta Selective Ligands Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. ...Authors: Manas, E.S. / Unwalla, R.J. / Xu, Z.B. / Malamas, M.S. / Miller, C.P. / Harris, H.A. / Hsiao, C. / Akopian, T. / Hum, W.T. / Malakian, K. / Wolfrom, S. / Bapat, A. / Bhat, R.A. / Stahl, M.L. / Somers, W.S. / Alvarez, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1x76.cif.gz | 104.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x76.ent.gz | 80.8 KB | Display | PDB format |
PDBx/mmJSON format | 1x76.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1x76_validation.pdf.gz | 491.2 KB | Display | wwPDB validaton report |
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Full document | 1x76_full_validation.pdf.gz | 501.9 KB | Display | |
Data in XML | 1x76_validation.xml.gz | 12 KB | Display | |
Data in CIF | 1x76_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/1x76 ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x76 | HTTPS FTP |
-Related 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: 27109.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, NR3A2, ESTRB / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q92731 #2: Protein/peptide | Mass: 1386.594 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: This sequence was derived from steroid receptor coactivator-1 References: UniProt: Q15788*PLUS #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: 2.66 Å3/Da / Density % sol: 0.52 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9 Details: PEG3350, Mg Formate, pH 5.90, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 14, 2000 |
Radiation | Monochromator: 0.9 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 23967 / Num. obs: 23879 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.86 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 21.8 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 5.9 / Num. unique all: 1136 / Rsym value: 0.243 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: COMPLEX STRUCTURE OF ER-BETA WITH GENESTEIN. Resolution: 2.2→14.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2287022.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.8117 Å2 / ksol: 0.363358 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→14.97 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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Xplor file |
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