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- EMDB-15708: Tomogram of a late endosome of A549-IFITM3 cell (Figure 1V) -

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Basic information

Entry
Database: EMDB / ID: EMD-15708
TitleTomogram of a late endosome of A549-IFITM3 cell (Figure 1V)
Map data
Sample
  • Cell: A549 cell
KeywordsIFITM3 / influenza A virus / membrane fusion / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / negative staining
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
DepositionSep 1, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15708.png

Downloads & links

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Map

FileDownload / File: emd_15708.map.gz / Format: CCP4 / Size: 346.7 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 10.3 Å
Density
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)43.291283 (±19.047779999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin9833-53
Dimensions18121967102
Spacing19671812102
CellA: 20260.1 Å / B: 18663.6 Å / C: 1050.6 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

EntireName: A549 cell
Components
  • Cell: A549 cell

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Supramolecule #1: A549 cell

SupramoleculeName: A549 cell / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.4
StainingType: POSITIVE / Material: 0.1 % uranyl acetate (UA)
Sugar embeddingMaterial: Lowicryl HM20 resin
VitrificationCryogen name: NITROGEN
High pressure freezingInstrument: OTHER
Details: The value given for _em_high_pressure_freezing.instrument is Leica EM AFS. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT', 'BAL-TEC HPM 010', 'LEICA EM PACT2', ...Details: The value given for _em_high_pressure_freezing.instrument is Leica EM AFS. This is not in a list of allowed values {'LEICA EM HPM100', 'LEICA EM PACT', 'BAL-TEC HPM 010', 'LEICA EM PACT2', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER'} so OTHER is written into the XML file.
SectioningUltramicrotomy - Instrument: Leica UC7 ultramicrotome / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 250

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: OTHER / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 121

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