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Yorodumi- PDB-4zi1: HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WIT... -
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-Basic information
Entry | Database: PDB / ID: 4zi1 | ||||||
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Title | HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE | ||||||
Components |
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Keywords | SIGNALING PROTEIN / ESTROGEN RECEPTOR BETA / BETA SELECTIVE / ERB | ||||||
Function / homology | Function and homology information receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / regulation of signal transduction / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / negative regulation of insulin receptor signaling pathway / steroid binding / ESR-mediated signaling ...receptor antagonist activity / nuclear steroid receptor activity / nuclear estrogen receptor activity / regulation of signal transduction / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / negative regulation of insulin receptor signaling pathway / steroid binding / ESR-mediated signaling / cellular response to estradiol stimulus / negative regulation of cell growth / positive regulation of DNA-binding transcription factor activity / Nuclear Receptor transcription pathway / transcription corepressor activity / Constitutive Signaling by Aberrant PI3K in Cancer / nuclear receptor activity / actin cytoskeleton / insulin receptor signaling pathway / PIP3 activates AKT signaling / cell-cell signaling / glucose homeostasis / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Extra-nuclear estrogen signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / extracellular space / zinc ion binding / nucleoplasm / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Kauppi, B. / Bonn, T. | ||||||
Citation | Journal: To Be Published Title: HUMAN ESTROGEN RECEPTOR BETA LIGAND-BINDING DOMAIN IN COMPLEX WITH KB095285 AND CIA12 COACTIVATOR PEPTIDE Authors: Kauppi, B. / Bonn, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zi1.cif.gz | 67.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zi1.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 4zi1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/4zi1 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/4zi1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Protein | Mass: 28029.234 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, UNP residues 262-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ESR2, ESTRB, NR3A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92731 |
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#2: Protein/peptide | Mass: 1286.430 Da / Num. of mol.: 1 / Fragment: 12mer PEPTIDE CIA12mod, UNP residues 341-352 / Mutation: Q343E, N347D / Source method: obtained synthetically Details: Two mutations were made to increase peptide solubility Source: (synth.) Homo sapiens (human) / References: UniProt: Q9HCD5 |
#3: Chemical | ChemComp-KB0 / |
#4: Water | ChemComp-HOH / |
Sequence details | CIA 12, 12-MER OF COACTIVATOR INDEPENDENT OF AF-2 FUNCTION PEPTIDE. DERIVED FROM NCOA5_HUMAN ...CIA 12, 12-MER OF COACTIVATO |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.6 Å3/Da / Density % sol: 65.1 % / Description: Bipyramides |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 10.5% (W/V) P6000, 1.75M NACL 0.1 M MES, PH 5.2, 12.5% (V/V) GLYCEROL, 2 TIMES EXCESS OF CIA12 PEPTIDE PH range: 5.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 12, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→19.98 Å / Num. obs: 23165 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 2.47 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.87 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.39 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.24 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: INTERNAL DATA Resolution: 2.1→19.98 Å / SU B: 7.075 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 43.341 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→19.98 Å
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LS refinement shell | Highest resolution: 2.1 Å |