[English] 日本語
Yorodumi- PDB-6fi4: Crystal structure of C-terminal modified Tau peptide-hybrid 3.2e ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fi4 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of C-terminal modified Tau peptide-hybrid 3.2e with 14-3-3sigma | |||||||||
Components |
| |||||||||
Keywords | STRUCTURAL PROTEIN / Tau 14-3-3 Alzheimer | |||||||||
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 / regulation of microtubule polymerization / keratinocyte development / keratinization / 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 / 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 / cytoplasmic microtubule organization / stress granule assembly / 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 / regulation of calcium-mediated signaling / RHO GTPases activate PKNs / 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 / cellular response to nerve growth factor stimulus / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of superoxide anion generation / release of cytochrome c from mitochondria / 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 / response to lead ion / microglial cell activation / negative regulation of protein kinase activity / regulation of synaptic plasticity / Hsp90 protein binding / 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: 2 Å | |||||||||
Authors | Andrei, S.A. / Meijer, F.A. / Ottmann, C. / Milroy, L.G. | |||||||||
Funding support | Netherlands, 1items
| |||||||||
Citation | Journal: ACS Chem Neurosci / Year: 2018 Title: Inhibition of 14-3-3/Tau by Hybrid Small-Molecule Peptides Operating via Two Different Binding Modes. Authors: Andrei, S.A. / Meijer, F.A. / Neves, J.F. / Brunsveld, L. / Landrieu, I. / Ottmann, C. / Milroy, L.G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fi4.cif.gz | 152.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fi4.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fi4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fi4 ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fi4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6fauC 6favC 6fawC 6fbwC 6fbyC 6fi5C 5hf3S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 26542.914 Da / Num. of mol.: 1 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: 591.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636*PLUS |
-Non-polymers , 5 types, 137 molecules
#3: Chemical | ChemComp-CA / |
---|---|
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-NA / |
#6: Chemical | ChemComp-60H / ( |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.06 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: 25% PEG400, 20 mM HEPES pH 7.1, 5% glycerol, 0.19 M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97793 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97793 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2→74.23 Å / Num. obs: 24922 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 39.66 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.018 / Rrim(I) all: 0.064 / Net I/σ(I): 21.2 / Num. measured all: 308845 / Scaling rejects: 34 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5hf3 Resolution: 2→74.23 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.32
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.89 Å2 / Biso mean: 59.6978 Å2 / Biso min: 34.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→74.23 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|