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- PDB-3ovl: Structure of an amyloid forming peptide VQIVYK from the TAU prote... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ovl | ||||||
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Title | Structure of an amyloid forming peptide VQIVYK from the TAU protein in complex with orange G | ||||||
![]() | Microtubule-associated protein | ||||||
![]() | PROTEIN FIBRIL / amyloid-like protofibril in complex with a small-molecule binder | ||||||
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 / axon development / central nervous system neuron development / regulation of microtubule polymerization / microtubule polymerization / minor groove of adenine-thymine-rich DNA binding / lipoprotein particle binding / dynactin binding / glial cell projection / apolipoprotein binding / negative regulation of mitochondrial membrane potential / protein polymerization / negative regulation of mitochondrial fission / axolemma / Caspase-mediated cleavage of cytoskeletal proteins / regulation of microtubule polymerization or depolymerization / positive regulation of axon extension / regulation of microtubule cytoskeleton organization / supramolecular fiber organization / Activation of AMPK downstream of NMDARs / stress granule assembly / regulation of cellular response to heat / cytoplasmic microtubule organization / regulation of calcium-mediated signaling / axon cytoplasm / positive regulation of microtubule polymerization / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / phosphatidylinositol binding / nuclear periphery / cellular response to nerve growth factor stimulus / positive regulation of superoxide anion generation / protein phosphatase 2A binding / regulation of autophagy / astrocyte activation / response to lead ion / synapse organization / microglial cell activation / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / cellular response to reactive oxygen species / microtubule cytoskeleton organization / SH3 domain binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / microtubule cytoskeleton / neuron projection development / cell-cell signaling / protein-macromolecule adaptor activity / actin binding / cellular response to heat / single-stranded DNA binding / protein-folding chaperone binding / cell body / growth cone / microtubule binding / double-stranded DNA binding / microtubule / amyloid fibril formation / sequence-specific DNA binding / dendritic spine / learning or memory / nuclear speck / neuron projection / membrane raft / axon / negative regulation of gene expression / neuronal cell body / DNA damage response / dendrite / protein kinase binding / enzyme binding / mitochondrion / DNA binding Similarity search - Function | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Landau, M. / Eisenberg, D. | ||||||
![]() | ![]() Title: Towards a pharmacophore for amyloid. Authors: Landau, M. / Sawaya, M.R. / Faull, K.F. / Laganowsky, A. / Jiang, L. / Sievers, S.A. / Liu, J. / Barrio, J.R. / Eisenberg, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 12.2 KB | Display | ![]() |
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PDB format | ![]() | 7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743.2 KB | Display | ![]() |
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Full document | ![]() | 743.4 KB | Display | |
Data in XML | ![]() | 3.1 KB | Display | |
Data in CIF | ![]() | 3.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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 on special symmetry positions |
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Details | The biological unit is a pair of beta sheets with orange G interrelating between two pairs of sheets. One sheet is constructed from chain A and unit cell translations along the b direction (i.e. X,Y+1,Z; X,Y+2,Z; X,Y+3,Z, etc.). The second sheet is constructed from -X-1/2,1/2+Y,-Z;-X-1/2,3/2+Y,-Z;-X-1/2,5/2+Y,-Z; etc. The other pairs of sheets will be contracted from -X,Y,-Z+1, -X,Y+1,-Z+1,-X,Y+2,-Z+1; etc. and from X+1/2,1/2+Y,Z+1, X+1/2,3/2+Y,Z+1, X+1/2,5/2+Y,Z+1; etc. |
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Components
#1: Protein/peptide | Mass: 749.917 Da / Num. of mol.: 1 / Fragment: VQIVYK (residues 306-311) / Source method: obtained synthetically / Details: VQIVYK (residues 306-311) from Tau, synthesized / References: UniProt: P10636 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACY / | #4: Chemical | ChemComp-ORA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.66 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: reservoir contained 0.1M Zinc Acetate dihydrate, 18% PEG 3350, vapor diffusion, hanging drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 17, 2008 | ||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→90 Å / Num. all: 587 / Num. obs: 587 / % possible obs: 87.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.9 Å2 / Rmerge(I) obs: 0.179 / Χ2: 1.071 / Net I/σ(I): 4.5 | ||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: ![]() 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: 36.92 Å2 / Biso mean: 20.2828 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.81→26.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.805→2.017 Å / Total num. of bins used: 5
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