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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
DescriptorMicrotubule-associated protein tau
KeywordsPROTEIN FIBRIL / TAU / AMYLOID / CROSS-BETA / BETA-HELIX
Specimen sourceHomo sapiens / human
MethodElectron microscopy (3.5 Å resolution / Tissue / Helical)
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.
CitationNature, 2017, 547, 185-190

Nature, 2017, 547, 185-190 Yorodumi Papers
Cryo-EM structures of tau filaments from Alzheimer's disease.
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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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: Polypeptide(L)
Microtubule-associated protein tau / 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

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Sample preparation

ComponentName: Tau from brain / Type: TISSUE / Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Homo sapiens
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 FIELD / 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 scansDimension width: 3710 / Dimension height: 3710 / Movie frames/image: 20 / Used frames/image: 2-20

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Processing

EM software
IDNameVersionCategoryImage processing IDFitting ID
1RELION2.0PARTICLE SELECTION1
4GctfCTF CORRECTION1
7CootMODEL FITTING1
9REFMACMODEL REFINEMENT1
10RELION2.0INITIAL EULER ASSIGNMENT1
11RELION2.0FINAL EULER ASSIGNMENT1
12RELION2.0CLASSIFICATION1
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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