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Yorodumi- EMDB-17649: Cryo-EM structure of the Emiliania huxleyi virus 201 (EhV-201) vi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-17649 | |||||||||
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Title | Cryo-EM structure of the Emiliania huxleyi virus 201 (EhV-201) virion vertex with a diameter of 50 nm. | |||||||||
Map data | main map | |||||||||
Sample |
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Keywords | cryo-EM / subtomogram averaging / EhV-201 / enveloped virus / capsid / major capsid protein / VIRUS | |||||||||
Biological species | Emiliania huxleyi virus 201 | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 13.0 Å | |||||||||
Authors | Homola M / Buttner CR / Fuzik T / Novacek J / Chaillet M / Forster F / Plevka P | |||||||||
Funding support | Czech Republic, European Union, 2 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structure and replication cycle of a virus infecting climate-modulating alga . Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H ...Authors: Miroslav Homola / Carina R Büttner / Tibor Füzik / Pavel Křepelka / Radka Holbová / Jiří Nováček / Marten L Chaillet / Jakub Žák / Danyil Grybchuk / Friedrich Förster / William H Wilson / Declan C Schroeder / Pavel Plevka / Abstract: The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses ...The globally distributed marine alga has cooling effect on the Earth's climate. The population density of is restricted by viruses, including virus 201 (EhV-201). Despite the impact of viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect by using fivefold vertices to bind to and fuse the virus' inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum-derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from cells, which enables the continuous release of virions by exocytosis. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_17649.map.gz | 2.3 MB | EMDB map data format | |
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Header (meta data) | emd-17649-v30.xml emd-17649.xml | 25.7 KB 25.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_17649_fsc.xml | 5.9 KB | Display | FSC data file |
Images | emd_17649.png | 131.3 KB | ||
Masks | emd_17649_msk_1.map | 8 MB | Mask map | |
Filedesc metadata | emd-17649.cif.gz | 5.5 KB | ||
Others | emd_17649_additional_1.map.gz emd_17649_additional_2.map.gz emd_17649_additional_3.map.gz emd_17649_half_map_1.map.gz emd_17649_half_map_2.map.gz | 1 MB 36.9 KB 5.9 MB 5.9 MB 5.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-17649 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17649 | HTTPS FTP |
-Validation report
Summary document | emd_17649_validation.pdf.gz | 841.6 KB | Display | EMDB validaton report |
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Full document | emd_17649_full_validation.pdf.gz | 841.2 KB | Display | |
Data in XML | emd_17649_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_17649_validation.cif.gz | 14 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17649 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-17649 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_17649.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | main map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.16 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_17649_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: main map - cut
File | emd_17649_additional_1.map | ||||||||||||
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Annotation | main map - cut | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: mask main map - cut
File | emd_17649_additional_2.map | ||||||||||||
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Annotation | mask main map - cut | ||||||||||||
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Density Histograms |
-Additional map: main map not masked refinement
File | emd_17649_additional_3.map | ||||||||||||
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Annotation | main map not masked refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1
File | emd_17649_half_map_1.map | ||||||||||||
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Annotation | Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2
File | emd_17649_half_map_2.map | ||||||||||||
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Annotation | Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Emiliania huxleyi virus 201
Entire | Name: Emiliania huxleyi virus 201 |
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Components |
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-Supramolecule #1: Emiliania huxleyi virus 201
Supramolecule | Name: Emiliania huxleyi virus 201 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: EhV-201 was propagated on a non-calcifying Emiliania huxleyi strain (CCPM 2090). NCBI-ID: 181210 / Sci species name: Emiliania huxleyi virus 201 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Emiliania huxleyi CCMP1516 (eukaryote) / Strain: CCMP 2090 |
Virus shell | Shell ID: 1 / Name: inner membrane |
Virus shell | Shell ID: 2 / Name: capsid / Diameter: 1990.0 Å / T number (triangulation number): 169 |
Virus shell | Shell ID: 3 / Name: outer membrane / Diameter: 2110.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 / Component - Name: sea salt Details: Sea salts (Sigma Aldrich - S9883) were dissolved in distilled water (40 g/L w/v), filtered through a 0.22 um filter, and pH adjusted to 8. |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 5e-05 kPa / Details: top side only |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV Details: Sample: 3.5 ul; Wait time: 10 s; Blot time: 3 s; Blot force: -2; Drain time: 0 s. |
Details | The viral sample was concentrated down to 1x10^10 plaque-forming units per ml (PFU ml^-1) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 77.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 4323 / Average exposure time: 1.5 sec. / Average electron dose: 2.42 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 30.0 µm / Calibrated defocus max: 4.0 µm / Calibrated defocus min: 2.0 µm / Calibrated magnification: 42000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 42000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |