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Yorodumi- EMDB-5376: Structure of a transcribing cypovirus by cryo-electron microscopy -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5376 | |||||||||
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Title | Structure of a transcribing cypovirus by cryo-electron microscopy | |||||||||
Map data | This is an image of a surface rendered twofold view of transcribing CPV | |||||||||
Sample |
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Keywords | dsRNA virus Reoviridae transcribing cypovirus | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bombyx mori cypovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Yang C / Ji G / Liu H / Zhang K / Liu G / Sun F / Zhu P / Cheng L | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2012 Title: Cryo-EM structure of a transcribing cypovirus. Authors: Chongwen Yang / Gang Ji / Hongrong Liu / Kai Zhang / Guangqiao Liu / Fei Sun / Ping Zhu / Lingpeng Cheng / Abstract: Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription ...Double-stranded RNA viruses in the family Reoviridae are capable of transcribing and capping nascent mRNA within an icosahedral viral capsid that remains intact throughout repeated transcription cycles. However, how the highly coordinated mRNA transcription and capping process is facilitated by viral capsid proteins is still unknown. Cypovirus provides a good model system for studying the mRNA transcription and capping mechanism of viruses in the family Reoviridae. Here, we report a full backbone model of a transcribing cypovirus built from a near-atomic-resolution density map by cryoelectron microscopy. Compared with the structure of a nontranscribing cypovirus, the major capsid proteins of transcribing cypovirus undergo a series of conformational changes, giving rise to structural changes in the capsid shell: (i) an enlarged capsid chamber, which provides genomic RNA with more flexibility to move within the densely packed capsid, and (ii) a widened peripentonal channel in the capsid shell, which we confirmed to be a pathway for nascent mRNA. A rod-like structure attributable to a partially resolved nascent mRNA was observed in this channel. In addition, conformational change in the turret protein results in a relatively open turret at each fivefold axis. A GMP moiety, which is transferred to 5'-diphosphorylated mRNA during the mRNA capping reaction, was identified in the pocket-like guanylyltransferase domain of the turret protein. | |||||||||
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_5376.map.gz | 542.5 MB | EMDB map data format | |
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Header (meta data) | emd-5376-v30.xml emd-5376.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_5376_1.jpg | 163 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5376 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5376 | HTTPS FTP |
-Validation report
Summary document | emd_5376_validation.pdf.gz | 343.8 KB | Display | EMDB validaton report |
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Full document | emd_5376_full_validation.pdf.gz | 343.3 KB | Display | |
Data in XML | emd_5376_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5376 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5376 | HTTPS FTP |
-Related structure data
Related structure data | 3j17MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar 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_5376.map.gz / Format: CCP4 / Size: 695.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is an image of a surface rendered twofold view of transcribing CPV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.196 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 : transcribing cypovirus
Entire | Name: transcribing cypovirus |
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Components |
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-Supramolecule #1000: transcribing cypovirus
Supramolecule | Name: transcribing cypovirus / type: sample / ID: 1000 / Number unique components: 5 |
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-Supramolecule #1: Bombyx mori cypovirus 1
Supramolecule | Name: Bombyx mori cypovirus 1 / type: virus / ID: 1 / Name.synonym: cypovirus / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: OTHER / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: cypovirus |
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Host (natural) | Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 650 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Details: 300 mesh quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: Vitrification instrument: FEI Vitrobot Mark IV / Method: blotted for 4s |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 92 K |
Details | parallel beam |
Date | Jul 20, 2011 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 845 / Average electron dose: 22 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 125390 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder: Titan Krios / Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each image |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: IMIRS and ISAF / Number images used: 8000 |