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- EMDB-72174: Re-processing of EMPIAR-10230 - in-vivo Tau PHF -

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Basic information

Entry
Database: EMDB / ID: EMD-72174
TitleRe-processing of EMPIAR-10230 - in-vivo Tau PHF
Map data
Sample
  • Complex: Amyloid, Tau PHF
KeywordsAmyloid / Tau / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsSchaefer JH / Lander GC
Funding support United States, Germany, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS095892 United States
German Research Foundation (DFG)556478029 Germany
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2026
Title: Helical reconstruction of amyloids in cryoSPARC.
Authors: Jan Hannes Schaefer / Robert T O'Neill / Joseph P Donnelly / Evan T Powers / Jeffery W Kelly / Gabriel C Lander /
Abstract: Amyloid-mediated proteotoxicity underlies over 50 diseases. Cryo-EM establishes direct links between filament morphologies and pathology, although microbial functional amyloids illustrate that this ...Amyloid-mediated proteotoxicity underlies over 50 diseases. Cryo-EM establishes direct links between filament morphologies and pathology, although microbial functional amyloids illustrate that this fold can evolve to serve physiological roles, unlike their pathogenic counterparts. Despite the growing popularity of the processing software cryoSPARC for single-particle analyses, RELION remains the dominant software platform for performing helical reconstruction of amyloid structures, highlighting an area for further development. Here, we present comprehensive processing guidelines for helical reconstruction of helical amyloids using cryoSPARC. Through systematic reprocessing and validation of publicly deposited datasets, we demonstrate the current capabilities and identify the key limitations, emphasizing the need for amyloid-specific parameter optimization within cryoSPARC workflows. Our findings showcase a potential for developing unsupervised processing workflows to meet the demanding throughput requirements of time-resolved in vitro studies and large-scale compound-screening initiatives, thereby accelerating therapeutic drug development. Ultimately, our goal is to shift the focus of amyloid cryo-EM from computationally intensive processing challenges towards addressing fundamental biological questions that enhance our capacity for treatment discovery.
History
DepositionAug 15, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72174.png

Downloads & links

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Map

FileDownload / File: emd_72174.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.378
Minimum - Maximum-0.22934398 - 0.88781965
Average (Standard dev.)0.017283315 (±0.06846817)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72174_msk_1.map
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AxesZYX

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Half map: #1

Fileemd_72174_half_map_1.map
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Half map: #2

Fileemd_72174_half_map_2.map
Projections & Slices
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Sample components

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Entire : Amyloid, Tau PHF

EntireName: Amyloid, Tau PHF
Components
  • Complex: Amyloid, Tau PHF

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Supramolecule #1: Amyloid, Tau PHF

SupramoleculeName: Amyloid, Tau PHF / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.7 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 2.39 Å
Applied symmetry - Helical parameters - Δ&Phi: 179.45 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 74677
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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