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- EMDB-6377: A putative ATPase mediates RNA transcription and capping in a dsR... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-6377 | |||||||||
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Title | A putative ATPase mediates RNA transcription and capping in a dsRNA virus | |||||||||
![]() | Reconstruction of SGA-CPV | |||||||||
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![]() | Viral ATPase / histidine-mediated guanylyl transfer / conformational changes / regulation of transcription | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
![]() | Yu XK / Jiang JS / Sun JC / Zhou ZH | |||||||||
![]() | ![]() Title: A putative ATPase mediates RNA transcription and capping in a dsRNA virus. Authors: Xuekui Yu / Jiansen Jiang / Jingchen Sun / Z Hong Zhou / ![]() Abstract: mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high- ...mRNA transcription in dsRNA viruses is a highly regulated process but the mechanism of this regulation is not known. Here, by nucleoside triphosphatase (NTPase) assay and comparisons of six high-resolution (2.9-3.1 Å) cryo-electron microscopy structures of cytoplasmic polyhedrosis virus with bound ligands, we show that the large sub-domain of the guanylyltransferase (GTase) domain of the turret protein (TP) also has an ATP-binding site and is likely an ATPase. S-adenosyl-L-methionine (SAM) acts as a signal and binds the methylase-2 domain of TP to induce conformational change of the viral capsid, which in turn activates the putative ATPase. ATP binding/hydrolysis leads to an enlarged capsid for efficient mRNA synthesis, an open GTase domain for His217-mediated guanylyl transfer, and an open methylase-1 domain for SAM binding and methyl transfer. Taken together, our data support a role of the putative ATPase in mediating the activation of mRNA transcription and capping within the confines of the virus. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 538.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 9.6 KB 9.6 KB | Display Display | ![]() |
Images | ![]() ![]() | 77.7 KB 3.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 402.1 KB | Display | ![]() |
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Full document | ![]() | 401.7 KB | Display | |
Data in XML | ![]() | 9.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3jb3MC ![]() 6371C ![]() 6374C ![]() 6375C ![]() 6376C ![]() 6378C ![]() 3jayC ![]() 3jazC ![]() 3jb0C ![]() 3jb1C ![]() 3jb2C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of SGA-CPV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.104 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Cytoplasmic polyhedrosis virus with SAM, GTP and ATP
Entire | Name: Cytoplasmic polyhedrosis virus with SAM, GTP and ATP |
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Components |
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-Supramolecule #1000: Cytoplasmic polyhedrosis virus with SAM, GTP and ATP
Supramolecule | Name: Cytoplasmic polyhedrosis virus with SAM, GTP and ATP / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 1 |
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-Supramolecule #1: Bombyx mori cypovirus 1
Supramolecule | Name: Bombyx mori cypovirus 1 / type: virus / ID: 1 / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: ![]() ![]() |
Virus shell | Shell ID: 1 / Diameter: 720 Å / T number (triangulation number): 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification. |
Date | Dec 20, 2012 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 60535 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.75 mm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: OTHER / Software - Name: IMIRS / Number images used: 40898 |