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- EMDB-45215: In situ structure of TDP43 fibrils -

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Basic information

Entry
Database: EMDB / ID: EMD-45215
TitleIn situ structure of TDP43 fibrils
Map data3D refinement of TDP43 filament
Sample
  • Cell: TDP43 filament
KeywordsRNA binding protein / RNA splicing / protein oligomer / helical filaments / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 27.0 Å
AuthorsChang ML / Erwin AL / Barmada SJ / Mosalaganti S
Funding support United States, 7 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10OD030275 United States
Other privateArnold and Mabel Beckmann Foundation award
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2GM150019 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS097542 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS113943 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1R56NS128110-01 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)P30AG072931 United States
CitationJournal: To Be Published
Title: In situ structure of TDP43 fibrils
Authors: Chang ML / Erwin AL / Barmada SJ / Mosalaganti S
History
DepositionJun 6, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45215.png

Downloads & links

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Map

FileDownload / File: emd_45215.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D refinement of TDP43 filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.47 Å/pix.
x 64 pix.
= 350.208 Å		5.47 Å/pix.
x 64 pix.
= 350.208 Å		5.47 Å/pix.
x 64 pix.
= 350.208 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.472 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.522
Minimum - Maximum-0.4605519 - 1.7864461
Average (Standard dev.)0.012753837 (±0.11447678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 350.208 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1 for TDP43 filament

Fileemd_45215_half_map_1.map
AnnotationHalf map 1 for TDP43 filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 for TDP43 filament

Fileemd_45215_half_map_2.map
AnnotationHalf map 2 for TDP43 filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TDP43 filament

EntireName: TDP43 filament
Components
  • Cell: TDP43 filament

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Supramolecule #1: TDP43 filament

SupramoleculeName: TDP43 filament / type: cell / ID: 1 / Parent: 0
Details: TDP43 filaments within cultured human iNeuron lysosomes
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.3
GridModel: Quantifoil / Material: GOLD / Mesh: 200 / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: Gold R1/4
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 310 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 3.27916 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: 4.0 µm / Nominal defocus min: 2.75 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.8 Å
Applied symmetry - Helical parameters - Δ&Phi: 1.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number subtomograms used: 3325
ExtractionNumber tomograms: 2 / Number images used: 8298 / Software - Name: Warp (ver. 1.1.0)
CTF correctionSoftware: (Name: Warp (ver. 1.1.0), RELION (ver. 3.1)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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