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- EMDB-57762: TMV Map using Pulsed Illumination -

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Basic information

Entry
Database: EMDB / ID: EMD-57762
TitleTMV Map using Pulsed Illumination
Map data
Sample
  • Virus: Tobacco mosaic virus
KeywordsTobacco Mosaic Virus / VIRUS
Biological speciesTobacco mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 5.62 Å
AuthorsKumar V / Radecke J / Chinmaya KV / Mohammed I / Ferreira RC / Harder D / Fotiadis D / Stahlberg H
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Citation
Journal: Nat Commun / Year: 2026
Title: Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules.
Authors: Vishal Kumar / Julika Radecke / Chinmaya K V / Inayathulla Mohammed / Ricardo C Guerrero-Ferreira / Daniel Harder / Dimitrios Fotiadis / Henning Stahlberg /
Abstract: Radiation damage remains a fundamental limitation in cryo-electron microscopy (cryo-EM), constraining the total electron dose that can be used and thus limiting high-resolution imaging of biological ...Radiation damage remains a fundamental limitation in cryo-electron microscopy (cryo-EM), constraining the total electron dose that can be used and thus limiting high-resolution imaging of biological specimens. Recent studies have proposed that temporally structured or pulsed electron beams could reduce radiation damage by allowing time for energy dissipation between individual electron interactions. To evaluate this hypothesis, we present a systematic investigation using a radiofrequency (RF) driven 300 kV Titan Krios microscope equipped with a cold field emission gun (c-FEG) to generate pulsed electron beams for specimens under cryogenic conditions. We compare radiation damage in three representative samples: paraffin 2D crystals, bacteriorhodopsin (purple membrane) 2D crystals, and plunge-frozen tobacco mosaic virus (TMV) in vitreous ice, under both pulsed and conventional ( = random) illumination, while keeping all other imaging conditions constant. Radiation damage is quantified by tracking the decay of computed diffraction intensities to determine the critical dose (N). We observe no statistically significant difference in critical dose between pulsed and random illumination across all 3 samples. Our findings provide a critical reference point for future development and evaluation of temporally modulated electron sources in cryo-EM instrumentation.
#1: Journal: To Be Published
Title: Pulsed-electron illumination does not reduce beam damage for imaging biological macromolecules
Authors: Kumar V / Radecke J / Chinmaya KV / Mohammed I / Ferreira RC / Harder D / Fotiadis D / Stahlberg H
History
DepositionApr 24, 2026-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57762.png

Downloads & links

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Map

FileDownload / File: emd_57762.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 512 pix.
= 331.52 Å		0.65 Å/pix.
x 512 pix.
= 331.52 Å		0.65 Å/pix.
x 512 pix.
= 331.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6475 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.009379818 - 0.015740812
Average (Standard dev.)0.00039341324 (±0.0020874836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 331.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_57762_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_57762_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tobacco mosaic virus

EntireName: Tobacco mosaic virus
Components
  • Virus: Tobacco mosaic virus

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Supramolecule #1: Tobacco mosaic virus

SupramoleculeName: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 5.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 1.7 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: EMDB MAP
EMDB ID:

55006

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 29152
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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