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- EMDB-55006: Cryo-EM structure of Tobacco Mosaic Virus (TMV) prepared using th... -

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Basic information

Entry
Database: EMDB / ID: EMD-55006
TitleCryo-EM structure of Tobacco Mosaic Virus (TMV) prepared using the cryoWriter automated grid preparation system with spiral writing.
Map data
Sample
  • Virus: Tobacco mosaic virus
    • Protein or peptide: Tobacco mosaic virus (strain vulgare) (TMV)
Keywordsautomated grid preparation / single-particle cryo-EM / cryoWriter / TMV / helical reconstruction / VIRAL PROTEIN
Biological speciesTobacco mosaic virus (strain vulgare) (TMV) / Tobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 1.83 Å
AuthorsChinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
Funding support Switzerland, European Union, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation200021_200628 Switzerland
European Research Council (ERC)101118656European Union
CitationJournal: Nat Commun / Year: 2026
Title: CryoWriter: a robotic solution for improved Cryo-EM grid preparation.
Authors: Chinmaya Kv / Babatunde Ekundayo / Marta Di Fabrizio / Inayathulla Mohammed / Julika Radecke / Henning Stahlberg / Massimo Kube /
Abstract: Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a ...Cryo-electron microscopy (cryo-EM) structure determination relies on preparing thin, vitreous films of sample solution on EM grids. Cryo-EM is a mature technology, but preparing the grids remains a major bottleneck. Here, we evaluate the cryoWriter, a blotting-free, microfluidic grid-preparation robot that writes nanoliter volumes onto EM grids in a controlled environment. Using capillary-writing in spiral or line patterns, we prepared high-quality grids from minimal sample volumes and obtained near-atomic reconstructions for test specimens, including TMV, apoferritin, and the membrane protein TRPM4. We further demonstrate programmable deposition modes, such as writing the sample twice to boost particle density, or two-line writing for on-grid mixing to visualize time-resolved protein-ligand binding. In a challenging case (NrS-1 DNA polymerase), the cryoWriter grids exhibited reduced orientation bias relative to conventional blotting, enabling a more isotropic reconstruction. These results show that the cryoWriter provides a versatile platform for reproducible low volume cryo-EM grid preparation and for on-grid biochemical workflows.
History
DepositionSep 4, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55006.png

Downloads & links

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Map

FileDownload / File: emd_55006.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 512 pix.
= 328.704 Å		0.64 Å/pix.
x 512 pix.
= 328.704 Å		0.64 Å/pix.
x 512 pix.
= 328.704 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.642 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0935
Minimum - Maximum-0.13072123 - 0.4401523
Average (Standard dev.)0.0016539969 (±0.020445898)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 328.704 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_55006_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_55006_half_map_2.map
Projections & Slices
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Sample components

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Entire : Tobacco mosaic virus

EntireName: Tobacco mosaic virus
Components
  • Virus: Tobacco mosaic virus
    • Protein or peptide: Tobacco mosaic virus (strain vulgare) (TMV)

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Supramolecule #1: Tobacco mosaic virus

SupramoleculeName: Tobacco mosaic virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / 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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Macromolecule #1: Tobacco mosaic virus (strain vulgare) (TMV)

MacromoleculeName: Tobacco mosaic virus (strain vulgare) (TMV) / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Tobacco mosaic virus (strain vulgare) (TMV)
SequenceString:
XSYSITTPSQ FVFLSSAWA D PIELINLC TN ALGNQFQ TQQ ARTVVQ RQFS EVWKP SPQVT VRFP DSDFKV YRY NAVLDPL VT ALLGAFDT R NRIIEVENQ ANPTTAETLD ATRRVDDAT V AIRSAINN LI VELIRGT GSY NRSSFE SSSG LVWTS GPAT

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 290 K

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 5824 / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.85 µm / Nominal defocus min: 0.35000000000000003 µm / Nominal magnification: 270000
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: 1.4 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.035 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 1.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4) / Number images used: 95222
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 484223 / Software - Name: cryoSPARC
Startup modelType of model: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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