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- EMDB-16572: 1.85 angstrom resolution cryo-EM reconstruction of tobacco mosaic... -

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Basic information

Entry
Database: EMDB / ID: EMD-16572
Title1.85 angstrom resolution cryo-EM reconstruction of tobacco mosaic virus, imaged on a JEOL CryoARM 300 with Direct Electron Apollo camera.
Map dataReconstruction of tobacco mosaic virus
Sample
  • Virus: Tobacco mosaic virus
Biological speciesTobacco mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsBhella D / Love AJ / Streetley J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_PC_17135 United Kingdom
CitationJournal: To Be Published
Title: 1.85 angstrom resolution cryo-EM reconstruction of tobacco mosaic virus, imaged on a JEOL CryoARM 300 with Direct Electron Apollo camera.
Authors: Bhella D / Love AJ / Streetley J / Taliansky M / McGeachy K / Bukharova T
History
DepositionJan 31, 2023-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16572.png

Downloads & links

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Map

FileDownload / File: emd_16572.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of tobacco mosaic virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 750 pix.
= 387. Å		0.52 Å/pix.
x 750 pix.
= 387. Å		0.52 Å/pix.
x 750 pix.
= 387. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.516 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.029839857 - 0.05581958
Average (Standard dev.)2.6472382e-05 (±0.0012208814)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions750750750
Spacing750750750
CellA=B=C: 386.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Reconstruction of tobacco mosaic virus Half map 1

Fileemd_16572_half_map_1.map
AnnotationReconstruction of tobacco mosaic virus Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Reconstruction of tobacco mosaic virus Half map 2

Fileemd_16572_half_map_2.map
AnnotationReconstruction of tobacco mosaic virus Half map 2
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
Details: Infected leaf material was ground in phosphate buffer, cleared with chloroform and centrifuged (4 degrees C, 10000g) for 20mins. The supernatant was then precipitated overnight at 4 degrees ...Details: Infected leaf material was ground in phosphate buffer, cleared with chloroform and centrifuged (4 degrees C, 10000g) for 20mins. The supernatant was then precipitated overnight at 4 degrees C after adding both NaCl and PEG8000 to 1% and 2% (w/v) respectively. This was centrifuged at 4 degrees C 10000g for 20 mins, and pellets were resuspended in 25 mM Tris-HCl pH 7.8, prior to loading onto 20% sucrose cushions made up in this buffer. The cushions were centrifuged at 175,500g at 4 degrees C for 2 h and the subsequently resuspended in 0.01 M Tris-HCl buffer (pH 7.8) or water prior to centrifugation at 175,500g at 4 degrees C for 2 h. The pellets were resuspended and centrifuged again as before. The pellets were finally reconstituted in water with 0.02% sodium azide.
NCBI-ID: 12242 / Sci species name: Tobacco mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Nicotiana tabacum (common tobacco)

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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

Concentration24 mg/mL
BufferpH: 7 / Details: Not buffered - sample was in H2O
GridModel: C-flat / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 80000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 30 eV
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: DIRECT ELECTRON APOLLO (4k x 4k) / Digitization - Dimensions - Width: 4000 pixel / Digitization - Dimensions - Height: 4000 pixel / Average electron dose: 60.0 e/Å2
Details: Images collected in super-resolution mode (0.387 angstroms/pixel). Calibrated pixel size 0.774 angstroms/pixel.

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Image processing

Segment selectionNumber selected: 498539 / Software - Name: RELION (ver. 4)
Details: Particles were selected from micrographs with an initial CTFfit resolution estimate of better than five angstroms
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 4)
Final reconstructionApplied symmetry - Helical parameters - Δz: 1.39851 Å
Applied symmetry - Helical parameters - Δ&Phi: 22.0177 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 398831
FSC plot (resolution estimation)

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