+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5256 | |||||||||
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Title | 3.1 Angstrom cryoEM structure of cytoplasmic polyhedrosis virus | |||||||||
Map data | This is a cryoEM density map of cytoplasmic polyhedrosis virus | |||||||||
Sample |
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Keywords | cytoplasmic polyhedrosis virus / 3D reconstruction / cryoEM / full atom model | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Bombyx mori cypovirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 3.1 Å | |||||||||
Authors | Yu X / Ge P / Jiang J / Atanasov I / Zhou ZH | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Atomic model of CPV reveals the mechanism used by this single-shelled virus to economically carry out functions conserved in multishelled reoviruses. Authors: Xuekui Yu / Peng Ge / Jiansen Jiang / Ivo Atanasov / Z Hong Zhou / Abstract: Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we ...Unlike the multishelled viruses in the Reoviridae, cytoplasmic polyhedrosis virus (CPV) is single shelled, yet stable and fully capable of carrying out functions conserved within Reoviridae. Here, we report a 3.1 Å resolution cryo electron microscopy structure of CPV and derive its atomic model, consisting of 60 turret proteins (TPs), 120 each of capsid shell proteins (CSPs) and large protrusion proteins (LPPs). Two unique segments of CSP contribute to CPV's stability: an inserted protrusion domain interacting with neighboring proteins, and an N-anchor tying up CSPs together through strong interactions such as β sheet augmentation. Without the need to interact with outer shell proteins, LPP retains only the N-terminal two-third region containing a conserved helix-barrel core and interacts exclusively with CSP. TP is also simplified, containing only domains involved in RNA capping. Our results illustrate how CPV proteins have evolved in a coordinative manner to economically carry out their conserved functions. | |||||||||
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_5256.map.gz | 417.5 MB | EMDB map data format | |
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Header (meta data) | emd-5256-v30.xml emd-5256.xml | 10.3 KB 10.3 KB | Display Display | EMDB header |
Images | emd_5256_1.jpg | 361.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5256 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5256 | HTTPS FTP |
-Validation report
Summary document | emd_5256_validation.pdf.gz | 398.6 KB | Display | EMDB validaton report |
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Full document | emd_5256_full_validation.pdf.gz | 398.2 KB | Display | |
Data in XML | emd_5256_validation.xml.gz | 9.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5256 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5256 | HTTPS FTP |
-Related structure data
Related structure data | 3izxMC 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_5256.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a cryoEM density map of cytoplasmic polyhedrosis virus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : cytoplasmic polyhedrosis virus (CPV)
Entire | Name: cytoplasmic polyhedrosis virus (CPV) |
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Components |
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-Supramolecule #1000: cytoplasmic polyhedrosis virus (CPV)
Supramolecule | Name: cytoplasmic polyhedrosis virus (CPV) / type: sample / ID: 1000 / Details: CPV particles were purified from polyhedra. / Oligomeric state: Icosahedral particle / 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: cytoplasmic polyhedrosis virus / NCBI-ID: 110829 / Sci species name: Bombyx mori cypovirus 1 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: cytoplasmic polyhedrosis virus |
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Host (natural) | Organism: Bombyx mori (domestic silkworm) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Diameter: 730 Å |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL |
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Buffer | pH: 7.4 / Details: 10mM PBS |
Staining | Type: NEGATIVE / Details: Sample was not stained |
Grid | Details: holey carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 40 % / Chamber temperature: 90 K / Instrument: OTHER / Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: objective lens astigmatism was corrected at 150,000 magnification Legacy - Electron beam tilt params: 0 |
Details | Low dose |
Date | Jul 12, 2010 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 996 / Average electron dose: 25 e/Å2 / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.75 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | 645 micrographs that clearly showed signals beyond 6 angstrom in their spectra |
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CTF correction | Details: Each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS / Number images used: 28993 |