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- EMDB-46870: Recombinant AD PHF -

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Basic information

Entry
Database: EMDB / ID: EMD-46870
TitleRecombinant AD PHF
Map data
Sample
  • Complex: Truncated tau 297-391
KeywordsRecombinant Human Truncated Tau 297-391 200mM MgCl2 200 RPM 10mM PB DTT Type 4a Filament in original publication. / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsVaquer-Alicea J / Diamond MI / Kunach P
Funding support United States, 3 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RP220582 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1RF1AG065407-01A1 United States
Chan Zuckerberg Initiative2018-191983 (5022) United States
CitationJournal: Sci Adv / Year: 2025
Title: Functional classification of tauopathy strains reveals the role of protofilament core residues.
Authors: Jaime Vaquer-Alicea / Victor A Manon / Vaibhav Bommareddy / Peter Kunach / Ankit Gupta / Jim Monistrol / Valerie A Perez / Hung Tri Tran / Nil Saez-Calveras / Siling Du / Sushobhna Batra / ...Authors: Jaime Vaquer-Alicea / Victor A Manon / Vaibhav Bommareddy / Peter Kunach / Ankit Gupta / Jim Monistrol / Valerie A Perez / Hung Tri Tran / Nil Saez-Calveras / Siling Du / Sushobhna Batra / Daniel Stoddard / Charles L White / Lukasz A Joachimiak / Sarah H Shahmoradian / Marc I Diamond /
Abstract: Distinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells ...Distinct tau amyloid assemblies underlie diverse tauopathies but defy rapid classification. Cell and animal experiments indicate tau functions as a prion, as different strains propagated in cells cause unique, transmissible neuropathology after inoculation. Strain amplification requires compatibility of the monomer and amyloid template. We used cryo-electron microscopy to study one cell-based yellow fluorescent protein (YFP)-tagged strain, resolving its amyloid nature. We then used sequential alanine (Ala) substitution (scan) within tau repeat domain (RD) to measure incorporation to preexisting tau RD-YFP aggregates. This robustly discriminated strains, defining sequences critical for monomer incorporation. We then created 3R/4R or 4R wild-type RD (amino acids 246 to 408) biosensors. Ala scan of recombinant tau seeds with the Alzheimer's disease (AD) fold matched that of AD homogenate. We scanned 22 brain lysates comprising four tauopathies. This clustered cases by neuropathological syndrome, revealed the role of amino acids in protofilament folds, and allowed strain discrimination based on amino acid requirements for prion replication.
History
DepositionSep 4, 2024-
Header (metadata) releaseJan 8, 2025-
Map releaseJan 8, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46870.png

Downloads & links

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Map

FileDownload / File: emd_46870.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 340 pix.
= 282.2 Å		0.83 Å/pix.
x 340 pix.
= 282.2 Å		0.83 Å/pix.
x 340 pix.
= 282.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.011
Minimum - Maximum-0.020555614 - 0.04304163
Average (Standard dev.)0.0002894754 (±0.0021950607)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 282.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_46870_msk_1.map
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Additional map: #1

Fileemd_46870_additional_1.map
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Half map: #1

Fileemd_46870_half_map_1.map
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Half map: #2

Fileemd_46870_half_map_2.map
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Sample components

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Entire : Truncated tau 297-391

EntireName: Truncated tau 297-391
Components
  • Complex: Truncated tau 297-391

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Supramolecule #1: Truncated tau 297-391

SupramoleculeName: Truncated tau 297-391 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4 / Details: 10mM Phosphate Buffer 10mM DTT 200mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average exposure time: 4.5 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.375 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40664
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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