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- EMDB-18676: Cryo-ET of cryo-FIB milled Ebola virus infected Huh7 cells at 22 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-18676
TitleCryo-ET of cryo-FIB milled Ebola virus infected Huh7 cells at 22 hours post infection
Map dataCryo-ET of cryo-FIB milled Ebola virus infected Huh7 cells at 22 hours post infection
Sample
  • Virus: Ebola virus - Mayinga, Zaire, 1976
KeywordsEbola virus / 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: To Be Published
Title: Molecular basis of the Ebola virus replication compartment maturation
Authors: Vallbracht M / Bodmer B / Fischer K / Makroczyova J / Winter S / Wachsmuth-Melm M / Hoenen T / Chlanda P
History
DepositionOct 18, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18676.png

Downloads & links

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Map

FileDownload / File: emd_18676.map.gz / Format: CCP4 / Size: 803.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET of cryo-FIB milled Ebola virus 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 162 pix.
= 1730.16 Å		10.68 Å/pix.
x 1366 pix.
= 14588.881 Å		10.68 Å/pix.
x 952 pix.
= 10167.36 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-116.784369999999996 - 83.551130000000001
Average (Standard dev.)21.979603000000001 (±8.772347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-165223-56
Dimensions1366952162
Spacing9521366162
CellA: 10167.36 Å / B: 14588.881 Å / C: 1730.16 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 / NCBI-ID: 128952 / Sci species name: Ebola virus - Mayinga, Zaire, 1976 / Virus type: VIRION / Virus isolate: OTHER / 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
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 / Nominal magnification: 33000
Sample stageCooling 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

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