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Yorodumi- PDB-4y32: Crystal structure of C-terminal modified Tau peptide-hybrid 109B ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4y32 | |||||||||
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Title | Crystal structure of C-terminal modified Tau peptide-hybrid 109B with 14-3-3sigma | |||||||||
Components |
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Keywords | SIGNALING PROTEIN / Peptide-hybrid / Inhibitor / Protein-protein interaction / Peptide binding protein / Adapter protein / 14-3-3 | |||||||||
Function / homology | Function and homology information plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex ...plus-end-directed organelle transport along microtubule / axonal transport / histone-dependent DNA binding / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / microtubule lateral binding / tubulin complex / phosphatidylinositol bisphosphate binding / main axon / regulation of long-term synaptic depression / negative regulation of kinase activity / negative regulation of tubulin deacetylation / generation of neurons / regulation of chromosome organization / positive regulation of protein localization / rRNA metabolic process / internal protein amino acid acetylation / regulation of mitochondrial fission / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / regulation of epidermal cell division / protein kinase C inhibitor activity / central nervous system neuron development / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / glial cell projection / negative regulation of mitochondrial membrane potential / apolipoprotein binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / protein polymerization / negative regulation of mitochondrial fission / axolemma / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / establishment of skin barrier / positive regulation of axon extension / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / stress granule assembly / cytoplasmic microtubule organization / regulation of cellular response to heat / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / axon cytoplasm / RHO GTPases activate PKNs / regulation of calcium-mediated signaling / positive regulation of microtubule polymerization / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / synapse assembly / protein export from nucleus / negative regulation of innate immune response / phosphatidylinositol binding / nuclear periphery / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / cellular response to nerve growth factor stimulus / release of cytochrome c from mitochondria / positive regulation of superoxide anion generation / positive regulation of protein export from nucleus / protein phosphatase 2A binding / stem cell proliferation / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / astrocyte activation / TP53 Regulates Metabolic Genes / response to lead ion / synapse organization / microglial cell activation / negative regulation of protein kinase activity / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / protein homooligomerization / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / neuron projection development Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | |||||||||
Authors | Bartel, M. / Milroy, L. / Bier, D. / Brunsveld, L. / Ottmann, C. | |||||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2015 Title: Stabilizer-Guided Inhibition of Protein-Protein Interactions. Authors: Milroy, L.G. / Bartel, M. / Henen, M.A. / Leysen, S. / Adriaans, J.M. / Brunsveld, L. / Landrieu, I. / Ottmann, C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y32.cif.gz | 131.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y32.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4y32.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/4y32 ftp://data.pdbj.org/pub/pdb/validation_reports/y3/4y32 | HTTPS FTP |
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-Related structure data
Related structure data | 4y3bC 4y5iC 5hf3C 4fl5S 4y3v 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
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947 #2: Protein/peptide | Mass: 851.861 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: The C-terminal proline contains chemical modifications Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS #3: Chemical | ChemComp-49F / ( | #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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 0.1 M Hepes/NaOH pH 7.1, 0.19 M CaCl2, 24% PEG 400, 5% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99983 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99983 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→47.477 Å / Num. obs: 63066 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.426 % / Biso Wilson estimate: 29.232 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.041 / Rrim(I) all: 0.044 / Χ2: 1.013 / Net I/σ(I): 29.72 / Num. measured all: 408200 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FL5 Resolution: 1.7→47.477 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.923 / SU B: 1.792 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.43 Å2 / Biso mean: 27.133 Å2 / Biso min: 11.15 Å2
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Refinement step | Cycle: final / Resolution: 1.7→47.477 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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