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- EMDB-15601: Cryotomogram of Vaccinia virus (WR) infected HeLa cell (mature vi... -

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Basic information

Entry
Database: EMDB / ID: EMD-15601
TitleCryotomogram of Vaccinia virus (WR) infected HeLa cell (mature virions)
Map data
Sample
  • Virus: Vaccinia virus WR
KeywordsPalisade / Lattice / A4 / VIRUS
Biological speciesVaccinia virus WR
Methodelectron tomography / cryo EM
AuthorsCalcraft T / Hernandez-Gonzalez M / Nans A / Rosenthal PB / Way M
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: PLoS Biol / Year: 2023
Title: A succession of two viral lattices drives vaccinia virus assembly.
Authors: Miguel Hernandez-Gonzalez / Thomas Calcraft / Andrea Nans / Peter B Rosenthal / Michael Way /
Abstract: During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped ...During its cytoplasmic replication, vaccinia virus assembles non-infectious spherical immature virions (IV) coated by a viral D13 lattice. Subsequently, IV mature into infectious brick-shaped intracellular mature virions (IMV) that lack D13. Here, we performed cryo-electron tomography (cryo-ET) of frozen-hydrated vaccinia-infected cells to structurally characterise the maturation process in situ. During IMV formation, a new viral core forms inside IV with a wall consisting of trimeric pillars arranged in a new pseudohexagonal lattice. This lattice appears as a palisade in cross-section. As maturation occurs, which involves a 50% reduction in particle volume, the viral membrane becomes corrugated as it adapts to the newly formed viral core in a process that does not appear to require membrane removal. Our study suggests that the length of this core is determined by the D13 lattice and that the consecutive D13 and palisade lattices control virion shape and dimensions during vaccinia assembly and maturation.
History
DepositionAug 16, 2022-
Header (metadata) releaseFeb 1, 2023-
Map releaseFeb 1, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15601.png

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Map

FileDownload / File: emd_15601.map.gz / Format: CCP4 / Size: 51.4 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 25.86 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-20.526509999999998 (±22.359095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-68
Dimensions619640136
Spacing640619136
CellA: 16550.4 Å / B: 16007.341 Å / C: 3516.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Vaccinia virus WR

EntireName: Vaccinia virus WR
Components
  • Virus: Vaccinia virus WR

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Supramolecule #1: Vaccinia virus WR

SupramoleculeName: Vaccinia virus WR / type: virus / ID: 1 / Parent: 0 / Details: A36-YdF deltaF11 / NCBI-ID: 10254 / Sci species name: Vaccinia virus WR / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 1.7 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: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 11600
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 reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 39

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