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Yorodumi- EMDB-15130: Tomogram of a late endosome of A549-IFITM3 cells infected with in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15130 | |||||||||
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Title | Tomogram of a late endosome of A549-IFITM3 cells infected with influenza A virus (Figure 4E) | |||||||||
Map data | Tomogram of a late endosome of A549-IFITM3 cells infected with influenza A virus (Figure 4E) | |||||||||
Sample |
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Keywords | IFITM3 / influenza A virus / membrane fusion / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Klein S / Chlanda P | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15130.map.gz | 4 GB | EMDB map data format | |
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Header (meta data) | emd-15130-v30.xml emd-15130.xml | 9.9 KB 9.9 KB | Display Display | EMDB header |
Images | emd_15130.png | 155.3 KB | ||
Filedesc metadata | emd-15130.cif.gz | 3.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15130 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15130 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_15130.map.gz / Format: CCP4 / Size: 7.4 GB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||||||||||||||
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Annotation | Tomogram of a late endosome of A549-IFITM3 cells infected with influenza A virus (Figure 4E) | ||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : A549 cell stably overexpressing IFITM3
Entire | Name: A549 cell stably overexpressing IFITM3 |
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Components |
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-Supramolecule #1: A549 cell stably overexpressing IFITM3
Supramolecule | Name: A549 cell stably overexpressing IFITM3 / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
Sectioning | Focused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.3 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 100 K / Focused ion beam - Initial thickness: 6000 / Focused ion beam - Final thickness: 150 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 0.004 µm / Nominal defocus min: 0.004 µm / Nominal magnification: 33000 |
Image recording | Film 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 |
-Image processing
Final reconstruction | Software - Name: SerialEM / Number images used: 41 |
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Details | The tomogram was denoised using cryoCARE. |