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- PDB-5o3t: Straight filament in Alzheimer's disease brain -

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Basic information

Database: PDB / ID: 5o3t
TitleStraight filament in Alzheimer's disease brain
ComponentsMicrotubule-associated protein tauTau protein
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 / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / histone-dependent DNA binding / 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 / neurofibrillary tangle assembly / positive regulation of diacylglycerol kinase activity / histone-dependent DNA binding / axonal transport / plus-end-directed organelle transport along microtubule / 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 / axon development / tubulin complex / 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 / intracellular distribution of mitochondria / negative regulation of tubulin deacetylation / AT DNA binding / regulation of mitochondrial fission / glial cell projection / central nervous system neuron development / regulation of calcium-mediated signaling / somatodendritic compartment / negative regulation of kinase activity / internal protein amino acid acetylation / cellular response to brain-derived neurotrophic factor stimulus / 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 / microtubule associated complex / positive regulation of axon extension / phosphatidylinositol binding / axon cytoplasm / apolipoprotein binding / regulation of microtubule cytoskeleton organization / microglial cell activation / synapse assembly / positive regulation of microtubule polymerization / nuclear periphery / synapse organization / amyloid fibril formation / regulation of autophagy / protein phosphatase 2A binding / microtubule cytoskeleton organization / astrocyte activation / cellular response to nerve growth factor stimulus / regulation of synaptic plasticity / cytoplasmic ribonucleoprotein granule / memory / positive regulation of superoxide anion generation / response to lead ion / Hsp90 protein binding / microtubule cytoskeleton / protein binding, bridging / cellular response to reactive oxygen species / cell body / cellular response to heat / regulation of cellular response to heat / single-stranded DNA binding / neuron projection development / activation of cysteine-type endopeptidase activity involved in apoptotic process / growth cone / positive regulation of neuron death / learning or memory / SH3 domain binding / 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 / membrane raft / axon / neuronal cell body
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 3.4 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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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

TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)51090
ΔGint (kcal/M)-228
Surface area (Å2)31680


#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

Experimental details


EM experimentAggregation state: TISSUE / Reconstruction method: helical reconstruction

Sample preparation

ComponentName: Tau / 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, 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

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: 0.2 sec. / Electron dose: 1.2 e/Å2
Details: images were collected in movie-mode at 5 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: 1560
EM imaging opticsEnergyfilter name: GIF Quantum / Energyfilter upper: 10 eV / Energyfilter lower: -10 eV
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 50


EM software
1RELION2.0particle selection
4GctfCTF correction
7Cootmodel fitting
9RELION2.0initial Euler assignment
10RELION2.0final Euler assignment
12RELION2.03D reconstruction
13REFMACmodel refinement
Helical symmertyAngular rotation/subunit: -1.05 deg. / Axial rise/subunit: 4.74 Å / Axial symmetry: C1
Particle selectionNumber of particles selected: 84701
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24689 / 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: 114 / 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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