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Yorodumi- PDB-4fl5: Crystal structure of human 14-3-3 sigma in complex with a Tau-pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fl5 | ||||||
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Title | Crystal structure of human 14-3-3 sigma in complex with a Tau-protein peptide surrounding pS214 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / Peptide binding protein | ||||||
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 / lipoprotein particle binding / intracellular distribution of mitochondria / axonal transport of mitochondrion / axon development / regulation of epidermal cell division / central nervous system neuron development / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / regulation of microtubule polymerization / keratinocyte development / keratinization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / negative regulation of mitochondrial membrane potential / dynactin binding / glial cell projection / 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 / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / negative regulation of keratinocyte proliferation / positive regulation of axon extension / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / supramolecular fiber organization / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Activation of AMPK downstream of NMDARs / regulation of microtubule cytoskeleton organization / 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 / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / RHO GTPases activate PKNs / 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 / cellular response to nerve growth factor stimulus / protein sequestering activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of superoxide anion generation / positive regulation of protein export from nucleus / protein phosphatase 2A binding / regulation of autophagy / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / astrocyte activation / TP53 Regulates Metabolic Genes / synapse organization / microglial cell activation / response to lead ion / Hsp90 protein binding / regulation of synaptic plasticity / negative regulation of protein kinase activity / PKR-mediated signaling / protein homooligomerization / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cytoplasmic ribonucleoprotein granule / memory / microtubule cytoskeleton organization / cellular response to reactive oxygen species / SH3 domain binding / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Schumacher, B. / Ottmann, C. | ||||||
Citation | Journal: FASEB J. / Year: 2015 Title: Involvement of 14-3-3 in tubulin instability and impaired axon development is mediated by Tau. Authors: Joo, Y. / Schumacher, B. / Landrieu, I. / Bartel, M. / Smet-Nocca, C. / Jang, A. / Choi, H.S. / Jeon, N.L. / Chang, K.A. / Kim, H.S. / Ottmann, C. / Suh, Y.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fl5.cif.gz | 126.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fl5.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 4fl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fl/4fl5 ftp://data.pdbj.org/pub/pdb/validation_reports/fl/4fl5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: x-1/2,-y-1/2,-z. |
-Components
-Protein / Protein/peptide , 2 types, 4 molecules ABPQ
#1: Protein | Mass: 26558.914 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HME1, SFN / Plasmid: pProEx HtB / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P31947 #2: Protein/peptide | Mass: 1133.168 Da / Num. of mol.: 2 / Fragment: UNP residues 527-536 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636 |
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-Non-polymers , 5 types, 544 molecules
#3: Chemical | #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-CA / #6: Chemical | #7: 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: 2.54 Å3/Da / Density % sol: 51.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 28% PEG 400, 5% glycerol, 2 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 25, 2009 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Number: 175180 / Rmerge(I) obs: 0.047 / D res high: 1.9 Å / Num. obs: 45097 / % possible obs: 99.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell | Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Num. obs: 6338 / % possible obs: 99.5 % / Rmerge(I) obs: 0.233 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→19.643 Å / Num. all: 45268 / Num. obs: 45097 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.532 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 21.78 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.64 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2117 / WRfactor Rwork: 0.1561 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8809 / SU B: 2.712 / SU ML: 0.082 / SU R Cruickshank DPI: 0.1332 / SU Rfree: 0.1355 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.87 Å2 / Biso mean: 17.8038 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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