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Yorodumi- EMDB-33406: D5 reconstruction of mud crab reovirus in transcriptionally activ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33406 | |||||||||
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Title | D5 reconstruction of mud crab reovirus in transcriptionally active state | |||||||||
Map data | Cryo-EM structure of tMCRV in D5 symmetry reveal its RdRp | |||||||||
Sample |
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Biological species | Scylla serrata reovirus SZ-2007 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Zhang Q / Gao Y | |||||||||
Funding support | China, 2 items
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Citation | Journal: PLoS Pathog / Year: 2023 Title: The structure of a 12-segmented dsRNA reovirus: New insights into capsid stabilization and organization. Authors: Qinfen Zhang / Yuanzhu Gao / Matthew L Baker / Shanshan Liu / Xudong Jia / Haidong Xu / Jianguo He / Jason T Kaelber / Shaoping Weng / Wen Jiang / Abstract: Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell ...Infecting a wide range of hosts, members of Reovirales (formerly Reoviridae) consist of a genome with different numbers of segmented double stranded RNAs (dsRNA) encapsulated by a proteinaceous shell and carry out genome replication and transcription inside the virion. Several cryo-electron microscopy (cryo-EM) structures of reoviruses with 9, 10 or 11 segmented dsRNA genomes have revealed insights into genome arrangement and transcription. However, the structure and genome arrangement of 12-segmented Reovirales members remain poorly understood. Using cryo-EM, we determined the structure of mud crab reovirus (MCRV), a 12-segmented dsRNA virus that is a putative member of Reovirales in the non-turreted Sedoreoviridae family, to near-atomic resolutions with icosahedral symmetry (3.1 Å) and without imposing icosahedral symmetry (3.4 Å). These structures revealed the organization of the major capsid proteins in two layers: an outer T = 13 layer consisting of VP12 trimers and unique VP11 clamps, and an inner T = 1 layer consisting of VP3 dimers. Additionally, ten RNA dependent RNA polymerases (RdRp) were well resolved just below the VP3 layer but were offset from the 5-fold axes and arranged with D5 symmetry, which has not previously been seen in other members of Reovirales. The N-termini of VP3 were shown to adopt four unique conformations; two of which anchor the RdRps, while the other two conformations are likely involved in genome organization and capsid stability. Taken together, these structures provide a new level of understanding for capsid stabilization and genome organization of segmented dsRNA viruses. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33406.map.gz | 889.3 MB | EMDB map data format | |
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Header (meta data) | emd-33406-v30.xml emd-33406.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_33406.png | 283.9 KB | ||
Others | emd_33406_half_map_1.map.gz emd_33406_half_map_2.map.gz | 313.9 MB 308.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33406 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33406 | HTTPS FTP |
-Validation report
Summary document | emd_33406_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_33406_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_33406_validation.xml.gz | 26.5 KB | Display | |
Data in CIF | emd_33406_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33406 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33406 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33406.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of tMCRV in D5 symmetry reveal its RdRp | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map 2
File | emd_33406_half_map_1.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_33406_half_map_2.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Scylla serrata reovirus SZ-2007
Entire | Name: Scylla serrata reovirus SZ-2007 |
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Components |
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-Supramolecule #1: Scylla serrata reovirus SZ-2007
Supramolecule | Name: Scylla serrata reovirus SZ-2007 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 458682 / Sci species name: Scylla serrata reovirus SZ-2007 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Scylla serrata (giant mud crab) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 3.0 µm / Calibrated defocus min: 0.3 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.3 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21945 |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |