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- PDB-5o3o: Pronase-treated paired helical filament in Alzheimer's disease brain -

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Basic information

Entry
Database: PDB / ID: 5o3o
TitlePronase-treated paired helical filament in Alzheimer's disease brain
ComponentsMicrotubule-associated protein tauTau protein
KeywordsPROTEIN FIBRIL / TAU / AMYLOID / CROSS-BETA / BETA-HELIX
Function / homologyCaspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / positive regulation of diacylglycerol kinase activity / plus-end-directed organelle transport along microtubule / neurofibrillary tangle assembly / axonal transport ...Caspase-mediated cleavage of cytoskeletal proteins / Tau and MAP proteins tubulin-binding repeat profile. / Tau and MAP proteins tubulin-binding repeat signature. / Tau and MAP protein, tubulin-binding repeat / Microtubule-associated protein Tau / Microtubule associated protein, tubulin-binding repeat / positive regulation of diacylglycerol kinase activity / plus-end-directed organelle transport along microtubule / neurofibrillary tangle assembly / axonal transport / histone-dependent DNA binding / negative regulation of establishment of protein localization to mitochondrion / neurofibrillary tangle / positive regulation of protein localization to synapse / phosphatidylinositol bisphosphate binding / regulation of chromosome organization / rRNA metabolic process / negative regulation of mitochondrial membrane potential / regulation of long term synaptic depression / tubulin complex / axon development / microtubule lateral binding / negative regulation of mitochondrial fission / microtubule polymerization / generation of neurons / lipoprotein particle binding / positive regulation of cellular protein localization / axonal transport of mitochondrion / negative regulation of tubulin deacetylation / intracellular distribution of mitochondria / AT DNA binding / regulation of mitochondrial fission / central nervous system neuron development / regulation of calcium-mediated signaling / somatodendritic compartment / negative regulation of kinase activity / cellular response to brain-derived neurotrophic factor stimulus / internal protein amino acid acetylation / regulation of microtubule polymerization / receptor ligand activity / dynactin binding / regulation of microtubule polymerization or depolymerization / supramolecular fiber organization / axolemma / stress granule assembly / cytoplasmic microtubule organization / main axon / regulation of response to DNA damage stimulus / synapse assembly / microtubule associated complex / positive regulation of axon extension / phosphatidylinositol binding / axon cytoplasm / apolipoprotein binding / protein phosphatase 2A binding / regulation of microtubule cytoskeleton organization / microglial cell activation / positive regulation of microtubule polymerization / nuclear periphery / synapse organization / amyloid fibril formation / regulation of autophagy / microtubule cytoskeleton organization / astrocyte activation / cellular response to nerve growth factor stimulus / cytoplasmic ribonucleoprotein granule / regulation of synaptic plasticity / Hsp90 protein binding / memory / positive regulation of superoxide anion generation / response to lead ion / protein binding, bridging / microtubule cytoskeleton / cellular response to reactive oxygen species / cell body / cellular response to heat / regulation of cellular response to heat / neuron projection development / single-stranded DNA binding / activation of cysteine-type endopeptidase activity involved in apoptotic process / growth cone / SH3 domain binding / positive regulation of neuron death / learning or memory / double-stranded DNA binding / actin binding / chaperone binding / cell-cell signaling / protein complex oligomerization / microtubule / protein homooligomerization / microtubule binding / dendritic spine / negative regulation of gene expression / sequence-specific DNA binding / nuclear speck / axon / neuronal cell body / dendrite / intracellular
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.5 Å resolution
AuthorsFitzpatrick, A.W.P. / Falcon, B. / He, S. / Murzin, A.G. / Murshudov, G. / Garringer, H.G. / Crowther, R.A. / Ghetti, B. / Goedert, M. / Scheres, S.H.W.
CitationJournal: Nature / Year: 2017
Title: Cryo-EM structures of tau filaments from Alzheimer's disease.
Authors: Anthony W P Fitzpatrick / Benjamin Falcon / Shaoda He / Alexey G Murzin / Garib Murshudov / Holly J Garringer / R Anthony Crowther / Bernardino Ghetti / Michel Goedert / Sjors H W Scheres
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 24, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collection / Source and taxonomy / Structure summaryem_imaging_optics / entity / entity_src_gen / entity_src_nat_em_imaging_optics.energyfilter_name / _entity.src_method

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Structure visualization

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Assembly

Deposited unit
A: Microtubule-associated protein tau
B: Microtubule-associated protein tau
C: Microtubule-associated protein tau
D: Microtubule-associated protein tau
E: Microtubule-associated protein tau
F: Microtubule-associated protein tau
G: Microtubule-associated protein tau
H: Microtubule-associated protein tau
I: Microtubule-associated protein tau
J: Microtubule-associated protein tau


Theoretical massNumber of molelcules
Total (without water)79,40110
Polyers79,40110
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)51350
ΔGint (kcal/M)-177
Surface area (Å2)31270
MethodPISA

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Components

#1: Protein/peptide
Microtubule-associated protein tau / Tau protein / Neurofibrillary tangle protein / Paired helical filament-tau / PHF-tau


Mass: 7940.141 Da / Num. of mol.: 10 / Fragment: UNP Residues 623-695 / Source: (natural) Homo sapiens (human) / References: UniProt: P10636

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Tau from brain / Type: TISSUE / Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
Buffer solutionDetails: 20 mM Tris-HCl pH 7.4 containing 100 mM NaCl / pH: 7.4
SpecimenConc.: 1 mg/ml
Details: Sarkosyl-insoluble material was extracted from grey matter of frontal and temporal cortex from the patients brain and treated with pronase, as described in the Methods section of the paper.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil Au R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Calibrated defocus min: 900 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.8 sec. / Electron dose: 2.5 e/Å2
Details: images were collected in movie-mode at 1.2 frames per second
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1 / Number of real images: 523
EM imaging opticsEnergyfilter name: GIF Quantum / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 20 / Used frames/image: 2-20

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Processing

EM software
IDNameVersionCategory
1RELION2.0particle selection
4GctfCTF correction
7Cootmodel fitting
9REFMACmodel refinement
10RELION2.0initial Euler assignment
11RELION2.0final Euler assignment
12RELION2.0classification
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 179.4 deg. / Axial rise/subunit: 2.36 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 66585
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 20778 / Number of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingDetails: Fourier-space refinement of the complete atomic model against the paired helical filament and straight filament maps was performed in REFMAC. A stack of three consecutive monomers from each of the protofilaments was refined to preserve nearest-neighbour interactions for the middle chain.
Overall b value: 106 / Ref protocol: AB INITIO MODEL / Ref space: RECIPROCAL / Target criteria: Fourier shell correlation
Atomic model buildingPDB-ID: 2RNM
Pdb chain ID: A / Pdb chain residue range: 226-242

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