+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2401 | |||||||||
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Title | Electron cryo-microscopy of emptied cricket parvovirus AdDNV | |||||||||
Map data | Reconstruction of emptied cricket parvovirus | |||||||||
Sample |
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Keywords | invertebrate parvovirus / emptied particle / parvovirus infection process | |||||||||
Biological species | Parvovirus | |||||||||
Method | single particle reconstruction / cryo EM | |||||||||
Authors | Geng M / XinZheng Z / Pavel P / Qian Y / Peter T / Michael GR | |||||||||
Citation | Journal: J Virol / Year: 2013 Title: The structure and host entry of an invertebrate parvovirus. Authors: Geng Meng / Xinzheng Zhang / Pavel Plevka / Qian Yu / Peter Tijssen / Michael G Rossmann / Abstract: The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate ...The 3.5-Å resolution X-ray crystal structure of mature cricket parvovirus (Acheta domesticus densovirus [AdDNV]) has been determined. Structural comparisons show that vertebrate and invertebrate parvoviruses have evolved independently, although there are common structural features among all parvovirus capsid proteins. It was shown that raising the temperature of the AdDNV particles caused a loss of their genomes. The structure of these emptied particles was determined by cryo-electron microscopy to 5.5-Å resolution, and the capsid structure was found to be the same as that for the full, mature virus except for the absence of the three ordered nucleotides observed in the crystal structure. The viral protein 1 (VP1) amino termini could be externalized without significant damage to the capsid. In vitro, this externalization of the VP1 amino termini is accompanied by the release of the viral genome. | |||||||||
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_2401.map.gz | 49 MB | EMDB map data format | |
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Header (meta data) | emd-2401-v30.xml emd-2401.xml | 6.2 KB 6.2 KB | Display Display | EMDB header |
Images | emd_2401.png | 326.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2401 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2401 | HTTPS FTP |
-Validation report
Summary document | emd_2401_validation.pdf.gz | 305.1 KB | Display | EMDB validaton report |
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Full document | emd_2401_full_validation.pdf.gz | 304.2 KB | Display | |
Data in XML | emd_2401_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2401 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2401 | HTTPS FTP |
-Related 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_2401.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of emptied cricket parvovirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 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 : Cricket parvovirus AdDNV
Entire | Name: Cricket parvovirus AdDNV |
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Components |
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-Supramolecule #1000: Cricket parvovirus AdDNV
Supramolecule | Name: Cricket parvovirus AdDNV / type: sample / ID: 1000 / Number unique components: 60 |
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-Supramolecule #1: Parvovirus
Supramolecule | Name: Parvovirus / type: virus / ID: 1 / NCBI-ID: 10781 / Sci species name: Parvovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: Acheta domesticus (house cricket) / synonym: INVERTEBRATES |
Virus shell | Shell ID: 1 / Name: vp4 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
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-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Date | Jan 5, 2013 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Number images used: 17000 |
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