+Open data
-Basic information
Entry | Database: PDB / ID: 3iz3 | ||||||
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Title | CryoEM structure of cytoplasmic polyhedrosis virus | ||||||
Components |
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Keywords | VIRUS / cryoelectron microscopy / cytoplasmic polyhedrosis virus / reovirus / transcription / icosahedral virus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bombyx mori cypovirus 1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Cheng, L. / Sun, J. / Zhang, K. / Mou, Z. / Huang, X. / Ji, G. / Sun, F. / Zhang, J. / Zhu, P. | ||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2011 Title: Atomic model of a cypovirus built from cryo-EM structure provides insight into the mechanism of mRNA capping. Authors: Lingpeng Cheng / Jingchen Sun / Kai Zhang / Zongjun Mou / Xiaoxing Huang / Gang Ji / Fei Sun / Jingqiang Zhang / Ping Zhu / Abstract: The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full ...The cytoplasmic polyhedrosis virus (CPV) from the family Reoviridae belongs to a subgroup of "turreted" reoviruses, in which the mRNA capping activity occurs in a pentameric turret. We report a full atomic model of CPV built from a 3D density map obtained using cryoelectron microscopy. The image data for the 3D reconstruction were acquired exclusively from a CCD camera. Our structure shows that the enzymatic domains of the pentameric turret of CPV are topologically conserved and that there are five unique channels connecting the guanylyltransferase and methyltransferase regions. This structural organization reveals how the channels guide nascent mRNA sequentially to guanylyltransferase, 7-N-methyltransferase, and 2'-O-methyltransferase in the turret, undergoing the highly coordinated mRNA capping activity. Furthermore, by fitting the deduced amino acid sequence of the protein VP5 to 120 large protrusion proteins on the CPV capsid shell, we confirmed that this protrusion protein is encoded by CPV RNA segment 7. | ||||||
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 | 3iz3.cif.gz | 726 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iz3.ent.gz | 594.9 KB | Display | PDB format |
PDBx/mmJSON format | 3iz3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iz3_validation.pdf.gz | 910.3 KB | Display | wwPDB validaton report |
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Full document | 3iz3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3iz3_validation.xml.gz | 116.7 KB | Display | |
Data in CIF | 3iz3_validation.cif.gz | 172.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iz/3iz3 ftp://data.pdbj.org/pub/pdb/validation_reports/iz/3iz3 | HTTPS FTP |
-Related structure data
Related structure data | 5233MC 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
#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: 148696.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: D3JWE6, UniProt: Q6TS43*PLUS #3: Protein | Mass: 32324.768 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bombyx mori cypovirus 1 / References: UniProt: C6K2M8 |
-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 | Name: Cytoplasmic Polyhedrosis Virus / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: NO / Host category: INVERTERBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Bombyx mori |
Buffer solution | Name: PBS / pH: 7.5 / Details: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 4 seconds before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Apr 10, 2010 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 75000 X / Nominal defocus max: 2.8 nm / Nominal defocus min: 0.8 nm / Cs: 2.7 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: OTHER / Specimen holder type: Titan Krios / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software | Name: IMIRS / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: Each micrograph | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: cross-common lines / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29000 / Nominal pixel size: 1.19 Å / Actual pixel size: 1.19 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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