+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22707 | ||||||||||||
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Title | BMV VLP assembled on oligoB with D6 symmetry | ||||||||||||
Map data | BMV VLP assembled on short oligo | ||||||||||||
Sample |
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Biological species | Brome mosaic virus | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Bond KM / Tsvetkova IB / Wang JC-Y / Jarrold MF / Dragnea B | ||||||||||||
Funding support | United States, 3 items
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Citation | Journal: Small / Year: 2020 Title: Virus Assembly Pathways: Straying Away but Not Too Far. Authors: Kevin Bond / Irina B Tsvetkova / Joseph Che-Yen Wang / Martin F Jarrold / Bogdan Dragnea / Abstract: Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate ...Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native one. However, they contain large native structure fragments that can be recycled to form BMV virions, should a viral genome become available. The existence of such structures suggest the possibility of a previously unknown regulatory pathway for the packaging process inside cells. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_22707.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-22707-v30.xml emd-22707.xml | 12.2 KB 12.2 KB | Display Display | EMDB header |
Images | emd_22707.png | 81.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22707 | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_22707.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | BMV VLP assembled on short oligo | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.68 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Brome mosaic virus
Entire | Name: Brome mosaic virus |
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Components |
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-Supramolecule #1: Brome mosaic virus
Supramolecule | Name: Brome mosaic virus / type: virus / ID: 1 / Parent: 0 Details: The purified BMV was disassembled and the RNA precipitated. The capsid protein was then assembled with 52 nt from a T-like region of the BMV RNA. NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Experimental: 2.5 MDa |
Virus shell | Shell ID: 1 / Name: capsid / Diameter: 220.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 4.5 / Component - Concentration: 100.0 mM / Component - Name: Ammonium acetate Details: 100 mM ammonium acetate that was pH adjusted to 4.5 with acetic acid |
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Grid | Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 15 s blotting time, 0 blotting force, and 100% humidity in Mark IV.. |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Startup model | Type of model: OTHER Details: The initial model was built de novo using the SGD algorithm implemented in Relion 3.0.8 with C1 symmetry |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08) |
Final reconstruction | Applied symmetry - Point group: D6 (2x6 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 29702 |