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Yorodumi- EMDB-15707: Tomogram of a late endosome of A549 cell treated with IFN-beta (F... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15707 | |||||||||
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Title | Tomogram of a late endosome of A549 cell treated with IFN-beta (Figure 1T) | |||||||||
Map data | ||||||||||
Sample |
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Keywords | IFITM3 / influenza A virus / membrane fusion / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | electron tomography / cryo EM / negative staining | |||||||||
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_15707.map.gz | 226.8 MB | EMDB map data format | |
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Header (meta data) | emd-15707-v30.xml emd-15707.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_15707.png | 186.1 KB | ||
Filedesc metadata | emd-15707.cif.gz | 3.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15707 | HTTPS FTP |
-Validation report
Summary document | emd_15707_validation.pdf.gz | 445.8 KB | Display | EMDB validaton report |
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Full document | emd_15707_full_validation.pdf.gz | 445.3 KB | Display | |
Data in XML | emd_15707_validation.xml.gz | 5 KB | Display | |
Data in CIF | emd_15707_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15707 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-15707 | 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_15707.map.gz / Format: CCP4 / Size: 293.8 MB / Type: IMAGE STORED AS SIGNED BYTE | ||||||||||||||||||||
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Voxel size | X=Y=Z: 10.3 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : A549 cell
Entire | Name: A549 cell |
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Components |
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-Supramolecule #1: A549 cell
Supramolecule | Name: A549 cell / type: cell / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | electron tomography |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 7.4 |
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Staining | Type: POSITIVE / Material: 0.1 % uranyl acetate (UA) |
Sugar embedding | Material: Lowicryl HM20 resin |
Vitrification | Cryogen name: NITROGEN |
High pressure freezing | Instrument: OTHER Details: The value given for _em_high_pressure_freezing.instrument is Leica EM AFS2. 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 AFS2. 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. |
Sectioning | Ultramicrotomy - Instrument: Leica UC7 ultramicrotome / Ultramicrotomy - Temperature: 293 K / Ultramicrotomy - Final thickness: 250 |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Film or detector model: OTHER / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.7000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Number images used: 121 |
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