+Open data
-Basic information
Entry | Database: PDB / ID: 3jay | ||||||
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Title | Atomic model of transcribing cytoplasmic polyhedrosis virus | ||||||
Components |
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Keywords | VIRUS / viral ATPase / histidine-mediated guanylyl transfer / conformational changes / regulation of transcription | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Yu, X.K. / Jiang, J.S. / Sun, J.C. / Zhou, Z.H. | ||||||
Citation | Journal: Elife / Year: 2015 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 |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jay.cif.gz | 827.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jay.ent.gz | 662.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jay_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3jay_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3jay_validation.xml.gz | 107.5 KB | Display | |
Data in CIF | 3jay_validation.cif.gz | 163.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jay ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jay | HTTPS FTP |
-Related structure data
Related structure data | 6378MC 6371C 6374C 6375C 6376C 6377C 3jazC 3jb0C 3jb1C 3jb2C 3jb3C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 3 types, 5 molecules ABCDE
#1: Protein | Mass: 120145.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q914N6 | ||
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#2: Protein | Mass: 148560.859 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: Q6TS43 #3: Protein | Mass: 49906.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: C6K2M8 |
-Non-polymers , 4 types, 5 molecules
#4: Chemical | #5: Chemical | ChemComp-ATP / | #6: Chemical | ChemComp-GTP / | #7: Chemical | ChemComp-MG / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Details of virus | Empty: NO / Enveloped: NO / Host category: INVERTEBRATES / Isolate: SPECIES / Type: VIRION | |||||||||||||||
Natural host | Organism: Bombyx mori | |||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK II) |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Nov 1, 2012 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 60535 X / Cs: 2.75 mm Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification. |
Specimen holder | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: IMIRS / Category: 3D reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Details: Each particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: Cross-common lines / Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41624 / Nominal pixel size: 1.104 Å / Actual pixel size: 1.104 Å / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3→39.032 Å / SU ML: 0.37 / σ(F): 2 / Phase error: 23.65 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 522.82 Å2 / Biso mean: 205.219 Å2 / Biso min: 20 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→39.032 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Total num. of bins used: 13 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Origin x: -41.9409 Å / Origin y: -68.7784 Å / Origin z: 261.2438 Å
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Refinement TLS group |
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