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- EMDB-18695: Cryo-ET of cryo-FIB milled Ebola virus-VP30-GFP infected Huh7 cel... -

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Basic information

Entry
Database: EMDB / ID: EMD-18695
TitleCryo-ET of cryo-FIB milled Ebola virus-VP30-GFP infected Huh7 cells at 22 hours post infection
Map dataCryo-ET of cryo-FIB milled Ebola virus-VP30-GFP infected Huh7 cells at 22 hours post infection.
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
KeywordsEbola virus infected cell / VIRUS
Biological speciesEbola virus - Mayinga, Zaire, 1976
Methodelectron tomography / cryo EM
AuthorsVallbracht M / Chlanda P
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)469065579 Germany
Other privateChica and Heinz Schaller Foundation Germany
CitationJournal: Cell / Year: 2025
Title: Nucleocapsid assembly drives Ebola viral factory maturation and dispersion.
Authors: Melina Vallbracht / Bianca S Bodmer / Konstantin Fischer / Jana Makroczyova / Sophie L Winter / Lisa Wendt / Moritz Wachsmuth-Melm / Thomas Hoenen / Petr Chlanda /
Abstract: Replication and genome encapsidation of many negative-sense RNA viruses take place in virus-induced membraneless organelles termed viral factories (VFs). Although liquid properties of VFs are ...Replication and genome encapsidation of many negative-sense RNA viruses take place in virus-induced membraneless organelles termed viral factories (VFs). Although liquid properties of VFs are believed to control the transition from genome replication to nucleocapsid (NC) assembly, VF maturation and interactions with the cellular environment remain elusive. Here, we apply in situ cryo-correlative light and electron tomography to follow NC assembly and changes in VF morphology and their liquid properties during Ebola virus infection. We show that viral NCs transition from loosely packed helical assemblies in early VFs to compact cylinders that arrange into highly organized parallel bundles later in infection. Early VFs associate with intermediate filaments and are devoid of other host material but become progressively accessible to cellular components. Our data suggest that this process is coupled to VF solidification, loss of sphericity, and dispersion and promotes cytoplasmic exposure of NCs to facilitate their transport to budding sites.
History
DepositionOct 19, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18695.png

Downloads & links

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Map

FileDownload / File: emd_18695.map.gz / Format: CCP4 / Size: 555 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET of cryo-FIB milled Ebola virus-VP30-GFP infected Huh7 cells at 22 hours post infection.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.68 Å/pix.
x 106 pix.
= 1132.08 Å		10.68 Å/pix.
x 1343 pix.
= 14343.24 Å		10.68 Å/pix.
x 1022 pix.
= 10914.96 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2.259643 - 1.0432419
Average (Standard dev.)-0.43568373 (±0.30490214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin49148
Dimensions13431022106
Spacing10221343106
CellA: 10914.96 Å / B: 14343.24 Å / C: 1132.0801 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ebola virus - Mayinga, Zaire, 1976

EntireName: Ebola virus - Mayinga, Zaire, 1976
Components
  • Virus: Ebola virus - Mayinga, Zaire, 1976

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Supramolecule #1: Ebola virus - Mayinga, Zaire, 1976

SupramoleculeName: Ebola virus - Mayinga, Zaire, 1976 / type: virus / ID: 1 / Parent: 0
Details: EBOLA-VP30-GFP Viruses was obtained using Ebola virus reverse genetics system.
NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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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: 7.4
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP / Details: Leica GP2.
DetailsCryo-ET of cryo-FIB milled Ebola virus-VP30-GFP infected Huh7 cells at 22 hours post infection
Cryo protectant10% glycerol
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.003 / Focused ion beam - Duration: 360 / Focused ion beam - Temperature: 90 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 200
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm
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 reconstructionSoftware - Name: IMOD / Number images used: 41
CTF correctionType: PHASE FLIPPING ONLY

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