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- EMDB-50152: Tau PHF subtomogram average relating to CS2 Figure 3i-j. -

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Basic information

Entry
Database: EMDB / ID: EMD-50152
TitleTau PHF subtomogram average relating to CS2 Figure 3i-j.
Map data
Sample
  • Tissue: Microtubule-associated protein tau
    • Protein or peptide: Microtubule-associated protein tau
KeywordsAmyloid / Filament / Alzheimer's / helical / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 8.7 Å
AuthorsJenkins J
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)RG.IMSB.122314 United Kingdom
CitationJournal: Nature / Year: 2024
Title: CryoET of β-amyloid and tau within postmortem Alzheimer's disease brain.
Authors: Madeleine A G Gilbert / Nayab Fatima / Joshua Jenkins / Thomas J O'Sullivan / Andreas Schertel / Yehuda Halfon / Martin Wilkinson / Tjado H J Morrema / Mirjam Geibel / Randy J Read / Neil A ...Authors: Madeleine A G Gilbert / Nayab Fatima / Joshua Jenkins / Thomas J O'Sullivan / Andreas Schertel / Yehuda Halfon / Martin Wilkinson / Tjado H J Morrema / Mirjam Geibel / Randy J Read / Neil A Ranson / Sheena E Radford / Jeroen J M Hoozemans / René A W Frank /
Abstract: A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures. In Alzheimer's disease, this is characterized by the ...A defining pathological feature of most neurodegenerative diseases is the assembly of proteins into amyloid that form disease-specific structures. In Alzheimer's disease, this is characterized by the deposition of β-amyloid and tau with disease-specific conformations. The in situ structure of amyloid in the human brain is unknown. Here, using cryo-fluorescence microscopy-targeted cryo-sectioning, cryo-focused ion beam-scanning electron microscopy lift-out and cryo-electron tomography, we determined in-tissue architectures of β-amyloid and tau pathology in a postmortem Alzheimer's disease donor brain. β-amyloid plaques contained a mixture of fibrils, some of which were branched, and protofilaments, arranged in parallel arrays and lattice-like structures. Extracellular vesicles and cuboidal particles defined the non-amyloid constituents of β-amyloid plaques. By contrast, tau inclusions formed parallel clusters of unbranched filaments. Subtomogram averaging a cluster of 136 tau filaments in a single tomogram revealed the polypeptide backbone conformation and filament polarity orientation of paired helical filaments within tissue. Filaments within most clusters were similar to each other, but were different between clusters, showing amyloid heterogeneity that is spatially organized by subcellular location. The in situ structural approaches outlined here for human donor tissues have applications to a broad range of neurodegenerative diseases.
History
DepositionApr 23, 2024-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50152.png

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Map

FileDownload / File: emd_50152.map.gz / Format: CCP4 / Size: 7.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
2.38 Å/pix.
x 126 pix.
= 299.88 Å		2.38 Å/pix.
x 126 pix.
= 299.88 Å		2.38 Å/pix.
x 126 pix.
= 299.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.38 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.004028675 - 0.011745775
Average (Standard dev.)0.000058210433 (±0.0011042394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions126126126
Spacing126126126
CellA=B=C: 299.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_50152_additional_1.map
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Additional map: #2

Fileemd_50152_additional_2.map
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Additional map: #3

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Half map: #1

Fileemd_50152_half_map_1.map
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Half map: #2

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Sample components

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Entire : Microtubule-associated protein tau

EntireName: Microtubule-associated protein tau
Components
  • Tissue: Microtubule-associated protein tau
    • Protein or peptide: Microtubule-associated protein tau

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Supramolecule #1: Microtubule-associated protein tau

SupramoleculeName: Microtubule-associated protein tau / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human) / Tissue: Brain

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Macromolecule #1: Microtubule-associated protein tau

MacromoleculeName: Microtubule-associated protein tau / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKST PTAEDVTAPL VDEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA G HVTQEPES GKVVQEGFLR EPGPPGLSHQ LMSGMPGAPL LPEGPREATR ...String:
MAEPRQEFEV MEDHAGTYGL GDRKDQGGYT MHQDQEGDTD AGLKESPLQT PTEDGSEEPG SETSDAKST PTAEDVTAPL VDEGAPGKQA AAQPHTEIPE GTTAEEAGIG DTPSLEDEAA G HVTQEPES GKVVQEGFLR EPGPPGLSHQ LMSGMPGAPL LPEGPREATR QPSGTGPEDT EG GRHAPEL LKHQLLGDLH QEGPPLKGAG GKERPGSKEE VDEDRDVDES SPQDSPPSKA SPA QDGRPP QTAAREATSI PGFPAEGAIP LPVDFLSKVS TEIPASEPDG PSVGRAKGQD APLE FTFHV EITPNVQKEQ AHSEEHLGRA AFPGAPGEGP EARGPSLGED TKEADLPEPS EKQPA AAPR GKPVSRVPQL KARMVSKSKD GTGSDDKKAK TSTRSSAKTL KNRPCLSPKH PTPGSS DPL IQPSSPAVCP EPPSSPKYVS SVTSRTGSSG AKEMKLKGAD GKTKIATPRG AAPPGQK GQ ANATRIPAKT PPAPKTPPSS GEPPKSGDRS GYSSPGSPGT PGSRSRTPSL PTPPTREP K KVAVVRTPPK SPSSAKSRLQ TAPVPMPDLK NVKSKIGSTE NLKHQPGGGK VQIINKKLD LSNVQSKCGS KDNIKHVPGG GSVQIVYKPV DLSKVTSKCG SLGNIHHKPG GGQVEVKSEK LDFKDRVQS KIGSLDNITH VPGGGNKKIE THKLTFRENA KAKTDHGAEI VYKSPVVSGD T SPRHLSNV SSTGSIDMVD SPQLATLADE VSASLAKQGL

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statetissue

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 5.0 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.72 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.86 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number subtomograms used: 4778
ExtractionNumber tomograms: 1 / Number images used: 13188
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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