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- EMDB-18241: doublet TMEM type 1 filament - individual 4, brainstem -

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Entry
Database: EMDB / ID: EMD-18241
Titledoublet TMEM type 1 filament - individual 4, brainstem
Map data
Sample
  • Tissue: doublet TMEM106B type 1 filament - individual 4, brainstem
Keywordsamyloid / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsTetter S / Ryskeldi-Falcon B
Funding support United Kingdom, Switzerland, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/25 United Kingdom
Swiss National Science FoundationP500PB_206890 Switzerland
Alzheimers Research UK (ARUK)ARUK-RS2019-001 United Kingdom
Leverhulme TrustECF-2022-610 United Kingdom
CitationJournal: Nature / Year: 2024
Title: TAF15 amyloid filaments in frontotemporal lobar degeneration.
Authors: Stephan Tetter / Diana Arseni / Alexey G Murzin / Yazead Buhidma / Sew Y Peak-Chew / Holly J Garringer / Kathy L Newell / Ruben Vidal / Liana G Apostolova / Tammaryn Lashley / Bernardino ...Authors: Stephan Tetter / Diana Arseni / Alexey G Murzin / Yazead Buhidma / Sew Y Peak-Chew / Holly J Garringer / Kathy L Newell / Ruben Vidal / Liana G Apostolova / Tammaryn Lashley / Bernardino Ghetti / Benjamin Ryskeldi-Falcon /
Abstract: Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders. The ...Frontotemporal lobar degeneration (FTLD) causes frontotemporal dementia (FTD), the most common form of dementia after Alzheimer's disease, and is often also associated with motor disorders. The pathological hallmarks of FTLD are neuronal inclusions of specific, abnormally assembled proteins. In the majority of cases the inclusions contain amyloid filament assemblies of TAR DNA-binding protein 43 (TDP-43) or tau, with distinct filament structures characterizing different FTLD subtypes. The presence of amyloid filaments and their identities and structures in the remaining approximately 10% of FTLD cases are unknown but are widely believed to be composed of the protein fused in sarcoma (FUS, also known as translocated in liposarcoma). As such, these cases are commonly referred to as FTLD-FUS. Here we used cryogenic electron microscopy (cryo-EM) to determine the structures of amyloid filaments extracted from the prefrontal and temporal cortices of four individuals with FTLD-FUS. Surprisingly, we found abundant amyloid filaments of the FUS homologue TATA-binding protein-associated factor 15 (TAF15, also known as TATA-binding protein-associated factor 2N) rather than of FUS itself. The filament fold is formed from residues 7-99 in the low-complexity domain (LCD) of TAF15 and was identical between individuals. Furthermore, we found TAF15 filaments with the same fold in the motor cortex and brainstem of two of the individuals, both showing upper and lower motor neuron pathology. The formation of TAF15 amyloid filaments with a characteristic fold in FTLD establishes TAF15 proteinopathy in neurodegenerative disease. The structure of TAF15 amyloid filaments provides a basis for the development of model systems of neurodegenerative disease, as well as for the design of diagnostic and therapeutic tools targeting TAF15 proteinopathy.
History
DepositionAug 17, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateFeb 7, 2024-
Current statusFeb 7, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18241.png

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Map

FileDownload / File: emd_18241.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.824 Å
Density
Contour LevelBy AUTHOR: 0.00447
Minimum - Maximum-0.013809077 - 0.024343139
Average (Standard dev.)0.000037479113 (±0.0006348031)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 421.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18241_msk_1.map
Projections & Slices
AxesZYX

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Half map: #1

Fileemd_18241_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_18241_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : doublet TMEM106B type 1 filament - individual 4, brainstem

EntireName: doublet TMEM106B type 1 filament - individual 4, brainstem
Components
  • Tissue: doublet TMEM106B type 1 filament - individual 4, brainstem

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Supramolecule #1: doublet TMEM106B type 1 filament - individual 4, brainstem

SupramoleculeName: doublet TMEM106B type 1 filament - individual 4, brainstem
type: tissue / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

14176

Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: -0.42 °
Applied symmetry - Helical parameters - Axial symmetry: C2 (2 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 29006
FSC plot (resolution estimation)

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