|Entry||Database: PDB / ID: 5mv5|
|Title||Structure of deformed wing virus, a honeybee pathogen|
|Descriptor||VP1, vp2, vp3|
|Keywords||VIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus / viral protein|
|Specimen source||Deformed wing virus / virus|
|Method||Electron microscopy (3.1 Å resolution / Particle / Single particle)|
|Authors||Skubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 3210-3215|
Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 3210-3215 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Jan 15, 2017 / Release: Apr 5, 2017|
Downloads & links
A: VP1x 60
A: VP1x 5
A: VP1x 6
Mass: 28679.273 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: L0CTV4
Mass: 28360.900 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: E0YTW0
Mass: 46697.582 Da / Num. of mol.: 1 / Source: (natural) Deformed wing virus / virus / References: UniProt: Q7TG18
|#4: Chemical||ChemComp-U / |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae. / Entity ID: 1, 2, 3 / Source: NATURAL|
|Molecular weight||Experimental value: NO|
|Source (natural)||Organism: Deformed wing virus|
|Details of virus||Empty: NO / Enveloped: NO / Virus isolate: OTHER / Virus type: VIRION|
|Natural host||Organism: Apis mellifera|
|Virus shell||Diameter: 390 Å / Triangulation number (T number): 3|
|Buffer solution||Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich|
|Specimen||Conc.: 2.5 mg/ml|
Details: Virus was incubated in high salt solution containing 0.8 M potassium dihydrogen phosphate, 0.8 M sodium dihydrogen phosphate, 0.1 M sodium HEPES, pH 7.5. After 12 hours incubation glutaraldehyde was added to final concentration 1%. After 1 hour was virus dialysed into PBS buffer.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
|Specimen support||Grid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Microscope model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 75000 / Calibrated magnification: 74235 / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 mm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Image recording||Average exposure time: 1 sec. / Electron dose: 21 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1|
|Image scans||Dimension width: 4096 / Dimension height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Number of particles selected: 75169|
|3D reconstruction||Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 27130 / Algorithm: FOURIER SPACE / Number of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Ref protocol: OTHER / Ref space: REAL / Target criteria: R-factor|
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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
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External links: The 2017 Nobel Prize in Chemistry - Press Release
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