+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31188 | |||||||||||||||||||||||||||
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Title | Icosahedral ISVP | |||||||||||||||||||||||||||
Map data | ||||||||||||||||||||||||||||
Sample | Mammalian orthoreovirus 3 Dearing != Mammalian orthoreovirus 3 Mammalian orthoreovirus 3 Dearing
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Function / homology | Function and homology information viral inner capsid / host cytoskeleton / 7-methylguanosine mRNA capping / viral genome replication / viral capsid / viral nucleocapsid / host cell cytoplasm / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / structural molecule activity / RNA binding Similarity search - Function | |||||||||||||||||||||||||||
Biological species | Mammalian orthoreovirus 3 | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||||||||||||||||||||
Authors | Zhou ZH / Pan M | |||||||||||||||||||||||||||
Funding support | United States, 8 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Asymmetric reconstruction of mammalian reovirus reveals interactions among RNA, transcriptional factor µ2 and capsid proteins. Authors: Muchen Pan / Ana L Alvarez-Cabrera / Joon S Kang / Lihua Wang / Chunhai Fan / Z Hong Zhou / Abstract: Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious ...Mammalian reovirus (MRV) is the prototypical member of genus Orthoreovirus of family Reoviridae. However, lacking high-resolution structures of its RNA polymerase cofactor μ2 and infectious particle, limits understanding of molecular interactions among proteins and RNA, and their contributions to virion assembly and RNA transcription. Here, we report the 3.3 Å-resolution asymmetric reconstruction of transcribing MRV and in situ atomic models of its capsid proteins, the asymmetrically attached RNA-dependent RNA polymerase (RdRp) λ3, and RdRp-bound nucleoside triphosphatase μ2 with a unique RNA-binding domain. We reveal molecular interactions among virion proteins and genomic and messenger RNA. Polymerase complexes in three Spinoreovirinae subfamily members are organized with different pseudo-D symmetries to engage their highly diversified genomes. The above interactions and those between symmetry-mismatched receptor-binding σ1 trimers and RNA-capping λ2 pentamers balance competing needs of capsid assembly, external protein removal, and allosteric triggering of endogenous RNA transcription, before, during and after infection, respectively. | |||||||||||||||||||||||||||
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_31188.map.gz | 403.1 MB | EMDB map data format | |
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Header (meta data) | emd-31188-v30.xml emd-31188.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_31188.png | 141.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31188 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31188 | HTTPS FTP |
-Validation report
Summary document | emd_31188_validation.pdf.gz | 388.4 KB | Display | EMDB validaton report |
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Full document | emd_31188_full_validation.pdf.gz | 388 KB | Display | |
Data in XML | emd_31188_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | emd_31188_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31188 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31188 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31188.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 4.28 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 : Mammalian orthoreovirus 3 Dearing
Entire | Name: Mammalian orthoreovirus 3 Dearing |
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Components |
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-Supramolecule #1: Mammalian orthoreovirus 3
Supramolecule | Name: Mammalian orthoreovirus 3 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 538123 / Sci species name: Mammalian orthoreovirus 3 / Sci species strain: Dearing / Virus type: VIRION / Virus isolate: SEROTYPE / 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: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14465 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |