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- PDB-4y3b: Crystal structure of C-terminal modified Tau peptide-hybrid 201D ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4y3b | ||||||
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Title | Crystal structure of C-terminal modified Tau peptide-hybrid 201D with 14-3-3sigma | ||||||
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![]() | SIGNALING PROTEIN / 14-3-3 FOLD / Tau / ALL ALPHA-HELICAL / ADAPTER PROTEIN / PROTEIN-PROTEIN INTERACTION / PEPTIDE BINDING PROTEIN | ||||||
Function / homology | ![]() 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / axon development / positive regulation of epidermal cell differentiation / keratinocyte development / central nervous system neuron development / keratinization / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / apolipoprotein binding / glial cell projection / negative regulation of mitochondrial membrane potential / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / protein polymerization / negative regulation of mitochondrial fission / phosphoserine residue binding / axolemma / 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 / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / stress granule assembly / negative regulation of stem cell proliferation / cytoplasmic microtubule organization / RHO GTPases activate PKNs / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / phosphatidylinositol binding / nuclear periphery / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / 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 / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / SH3 domain binding / microtubule cytoskeleton organization / activation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bartel, M. / Milroy, L.G. / Brunsveld, L. / Ottmann, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 126.6 KB | Display | ![]() |
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PDB format | ![]() | 96.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 423.2 KB | Display | ![]() |
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Full document | ![]() | 426.1 KB | Display | |
Data in XML | ![]() | 11.8 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y32C ![]() 4y5iC ![]() 5hf3C ![]() 4fl5S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() #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.) ![]() #3: Chemical | ChemComp-49F / ( | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.77 % |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 27, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→66.423 Å / Num. obs: 63066 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / 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: _
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4FL5 Resolution: 1.8→45.491 Å / SU ML: 0.15 / Cross valid method: NONE / σ(F): 1.99 / Phase error: 17.47 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 100.99 Å2 / Biso mean: 25.9192 Å2 / Biso min: 10.63 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→45.491 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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