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- EMDB-39712: 1.4A Tobacco Mosaic Virus (CryoSPARC processing from Falcon 4 data) -

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Basic information

Entry
Database: EMDB / ID: EMD-39712
Title1.4A Tobacco Mosaic Virus (CryoSPARC processing from Falcon 4 data)
Map dataTMV CryoSPARC Helical Refinement sharpened, symmeterised map
Sample
  • Virus: Tobacco mosaic virus
KeywordsHelical reconstruction / TMV / Virus
Biological speciesTobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 1.43 Å
AuthorsBurton-Smith RN / Murata K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: 1.4A Tobacco Mosaic Virus (CryoSPARC processing from Falcon 4 data) (to be published)
Authors: Burton-Smith RN / Murata K
History
DepositionApr 10, 2024-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 8, 2024-
Current statusMay 8, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39712.png

Downloads & links

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Map

FileDownload / File: emd_39712.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTMV CryoSPARC Helical Refinement sharpened, symmeterised map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.46 Å/pix.
x 768 pix.
= 353.28 Å		0.46 Å/pix.
x 768 pix.
= 353.28 Å		0.46 Å/pix.
x 768 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.46 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0919
Minimum - Maximum-0.44742578 - 0.61277986
Average (Standard dev.)0.0010659151 (±0.030622056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_39712_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TMV CryoSPARC Helical Refinement sharpened, UNsymmeterised map

Fileemd_39712_additional_1.map
AnnotationTMV CryoSPARC Helical Refinement sharpened, UNsymmeterised map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TMV CryoSPARC Helical Refinement UNsharpened, UNsymmeterised map

Fileemd_39712_additional_2.map
AnnotationTMV CryoSPARC Helical Refinement UNsharpened, UNsymmeterised map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: TMV CryoSPARC Helical Refinement UNsharpened, symmeterised map

Fileemd_39712_additional_3.map
AnnotationTMV CryoSPARC Helical Refinement UNsharpened, symmeterised map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TMV CryoSPARC Helical Refinement half map 2 (B)

Fileemd_39712_half_map_1.map
AnnotationTMV CryoSPARC Helical Refinement half map 2 (B)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: TMV CryoSPARC Helical Refinement half map 1 (A)

Fileemd_39712_half_map_2.map
AnnotationTMV CryoSPARC Helical Refinement half map 1 (A)
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: OTHER / Virus enveloped: No / Virus empty: Yes

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Average electron dose: 40.0 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: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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: 1.382 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.035 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 1.43 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 1601225
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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