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Yorodumi- PDB-4np8: Structure of an amyloid forming peptide VQIVYK from the second re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4np8 | |||||||||
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Title | Structure of an amyloid forming peptide VQIVYK from the second repeat region of tau (alternate polymorph) | |||||||||
Components | Microtubule-associated protein tau | |||||||||
Keywords | PROTEIN FIBRIL / amyloid-like protofibril | |||||||||
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 / positive regulation of protein localization / regulation of chromosome organization / 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 / apolipoprotein binding / glial cell projection / 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 / Activation of AMPK downstream of NMDARs / supramolecular fiber organization / regulation of cellular response to heat / stress granule assembly / 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 / microglial cell activation / synapse organization / Hsp90 protein binding / regulation of synaptic plasticity / PKR-mediated signaling / protein homooligomerization / memory / cytoplasmic ribonucleoprotein granule / SH3 domain binding / microtubule cytoskeleton organization / cellular response to reactive oxygen species / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 Å | |||||||||
Authors | Landau, M. / Eisenberg, D. / Sawaya, M.R. / Dannenberg, J. / Kobko, N. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2009 Title: Molecular mechanisms for protein-encoded inheritance. Authors: Wiltzius, J.J. / Landau, M. / Nelson, R. / Sawaya, M.R. / Apostol, M.I. / Goldschmidt, L. / Soriaga, A.B. / Cascio, D. / Rajashankar, K. / Eisenberg, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4np8.cif.gz | 9.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4np8.ent.gz | 5.5 KB | Display | PDB format |
PDBx/mmJSON format | 4np8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4np8_validation.pdf.gz | 372.6 KB | Display | wwPDB validaton report |
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Full document | 4np8_full_validation.pdf.gz | 372.6 KB | Display | |
Data in XML | 4np8_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 4np8_validation.cif.gz | 2.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/4np8 ftp://data.pdbj.org/pub/pdb/validation_reports/np/4np8 | HTTPS FTP |
-Related structure data
Related structure data | 3fodC 3fpoC 3fr1C 3fthC 3ftkC 3ftlC 3ftrC 3fvaC 2on9S 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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Details | The biological unit is a pair of beta 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 -1/2-X,1/2+Y,-Z; -1/2-X,3/2+Y,-Z; -1/2-X,5/2+Y,-Z; etc.). |
-Components
#1: Protein/peptide | Mass: 749.917 Da / Num. of mol.: 1 / Fragment: UNP residues 623-628 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10636 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.56 Å3/Da / Density % sol: 21.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: reservoir contained 14% iso-Propanol, 0.07M HEPES-Na pH 7.5, 0.14M Sodium Citrate, and 30% Glycerol, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 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: 1.5→90 Å / Num. all: 825 / Num. obs: 825 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 8.1 |
Reflection shell | Resolution: 1.5→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 4.7 / Num. unique all: 156 / % possible all: 82.1 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ON9 Resolution: 1.51→16.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.207 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8187 / SU B: 1.895 / SU ML: 0.065 / SU R Cruickshank DPI: 0.0982 / SU Rfree: 0.0894 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.089 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 26.57 Å2 / Biso mean: 7.5741 Å2 / Biso min: 3.8 Å2
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Refinement step | Cycle: LAST / Resolution: 1.51→16.78 Å /
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Refine LS restraints |
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LS refinement shell | Resolution: 1.508→1.547 Å / Total num. of bins used: 20
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