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Yorodumi- EMDB-21293: 3-fold sub-particle reconstruction V of brome mosaic virus (RNA 3... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21293 | |||||||||
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Title | 3-fold sub-particle reconstruction V of brome mosaic virus (RNA 3 and 4) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Brome mosaic virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
Authors | Beren C / Cui YX / Chakravarty A / Yang X / Rao ALN / Knobler CM / Zhou ZH / Gelbart WM | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Genome organization and interaction with capsid protein in a multipartite RNA virus. Authors: Christian Beren / Yanxiang Cui / Antara Chakravarty / Xue Yang / A L N Rao / Charles M Knobler / Z Hong Zhou / William M Gelbart / Abstract: We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a ...We report the asymmetric reconstruction of the single-stranded RNA (ssRNA) content in one of the three otherwise identical virions of a multipartite RNA virus, brome mosaic virus (BMV). We exploit a sample consisting exclusively of particles with the same RNA content-specifically, RNAs 3 and 4-assembled in planta by agrobacterium-mediated transient expression. We find that the interior of the particle is nearly empty, with most of the RNA genome situated at the capsid shell. However, this density is disordered in the sense that the RNA is not associated with any particular structure but rather, with an ensemble of secondary/tertiary structures that interact with the capsid protein. Our results illustrate a fundamental difference between the ssRNA organization in the multipartite BMV viral capsid and the monopartite bacteriophages MS2 and Qβ for which a dominant RNA conformation is found inside the assembled viral capsids, with RNA density conserved even at the center of the particle. This can be understood in the context of the differing demands on their respective lifecycles: BMV must package separately each of several different RNA molecules and has been shown to replicate and package them in isolated, membrane-bound, cytoplasmic complexes, whereas the bacteriophages exploit sequence-specific "packaging signals" throughout the viral RNA to package their monopartite genomes. | |||||||||
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_21293.map.gz | 11.7 MB | EMDB map data format | |
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Header (meta data) | emd-21293-v30.xml emd-21293.xml | 16.4 KB 16.4 KB | Display Display | EMDB header |
Images | emd_21293.png | 235.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21293 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21293 | HTTPS FTP |
-Validation report
Summary document | emd_21293_validation.pdf.gz | 78.7 KB | Display | EMDB validaton report |
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Full document | emd_21293_full_validation.pdf.gz | 77.7 KB | Display | |
Data in XML | emd_21293_validation.xml.gz | 493 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21293 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21293 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_21293.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 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 / Macromolecule list: #1-#3 / NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Average electron dose: 48.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: OTHER / Number images used: 283819 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |