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- EMDB-16133: Tomogram of a late endosome of A549 cell infected with influenza ... -

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Basic information

Entry
Database: EMDB / ID: EMD-16133
TitleTomogram of a late endosome of A549 cell infected with influenza A virus (Figure 6O)
Map data
Sample
  • Cell: A549 cell stably overexpressing IFITM3
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsKlein S / Chlanda P
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1129 Germany
CitationJournal: Cell Host Microbe / Year: 2023
Title: IFITM3 blocks influenza virus entry by sorting lipids and stabilizing hemifusion.
Authors: Steffen Klein / Gonen Golani / Fabio Lolicato / Carmen Lahr / Daniel Beyer / Alexia Herrmann / Moritz Wachsmuth-Melm / Nina Reddmann / Romy Brecht / Mehdi Hosseinzadeh / Androniki Kolovou / ...Authors: Steffen Klein / Gonen Golani / Fabio Lolicato / Carmen Lahr / Daniel Beyer / Alexia Herrmann / Moritz Wachsmuth-Melm / Nina Reddmann / Romy Brecht / Mehdi Hosseinzadeh / Androniki Kolovou / Jana Makroczyova / Sarah Peterl / Martin Schorb / Yannick Schwab / Britta Brügger / Walter Nickel / Ulrich S Schwarz / Petr Chlanda /
Abstract: Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically ...Interferon-induced transmembrane protein 3 (IFITM3) inhibits the entry of numerous viruses through undefined molecular mechanisms. IFITM3 localizes in the endosomal-lysosomal system and specifically affects virus fusion with target cell membranes. We found that IFITM3 induces local lipid sorting, resulting in an increased concentration of lipids disfavoring viral fusion at the hemifusion site. This increases the energy barrier for fusion pore formation and the hemifusion dwell time, promoting viral degradation in lysosomes. In situ cryo-electron tomography captured IFITM3-mediated arrest of influenza A virus membrane fusion. Observation of hemifusion diaphragms between viral particles and late endosomal membranes confirmed hemifusion stabilization as a molecular mechanism of IFITM3. The presence of the influenza fusion protein hemagglutinin in post-fusion conformation close to hemifusion sites further indicated that IFITM3 does not interfere with the viral fusion machinery. Collectively, these findings show that IFITM3 induces lipid sorting to stabilize hemifusion and prevent virus entry into target cells.
History
DepositionNov 13, 2022-
Header (metadata) releaseApr 19, 2023-
Map releaseApr 19, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16133.png

Downloads & links

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Map

FileDownload / File: emd_16133.map.gz / Format: CCP4 / Size: 714.3 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 8.013 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)-1.6142397 (±16.064835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-278278-143
Dimensions19201364286
Spacing13641920286
CellA: 10929.731 Å / B: 15384.959 Å / C: 2291.7178 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : A549 cell stably overexpressing IFITM3

EntireName: A549 cell stably overexpressing IFITM3
Components
  • Cell: A549 cell stably overexpressing IFITM3

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Supramolecule #1: A549 cell stably overexpressing IFITM3

SupramoleculeName: A549 cell stably overexpressing IFITM3 / type: cell / ID: 1 / Parent: 0
Source (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: 7.4
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 kV / Focused ion beam - Current: 0.3 nA / Focused ion beam - Duration: 600 sec. / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 6000 nm / Focused ion beam - Final thickness: 150 nm
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is ThermoFisher Aquilos. 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 33000
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: SerialEM / Number images used: 41

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