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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: To Be Published
Title: CryoWriter: A Robotic Solution for Improved Cryo-EM Grid Preparation
Authors: Chinmaya KV / Ekundayo B / Di Fabrizio M / Mohammed I / Radecke J / Stahlberg H / Kube M
History
DepositionSep 4, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55006_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
    • 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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