|Entry||Database: PDB / ID: 5mup|
|Title||Structure of deformed wing virus, a honeybee pathogen|
|Keywords||VIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus / bee pathogen|
|Function / homology|
Function and homology information
cysteine-type peptidase activity / host cell membrane / viral capsid / viral RNA genome replication / RNA helicase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / structural molecule activity / RNA binding / membrane / ATP binding
picornavirus capsid protein / RNA-directed RNA polymerase, C-terminal domain / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain ...picornavirus capsid protein / RNA-directed RNA polymerase, C-terminal domain / CRPV capsid protein like / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / P-loop containing nucleoside triphosphate hydrolase / Dicistrovirus, capsid-polyprotein, C-terminal / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / Picornavirus capsid / Helicase, superfamily 3, single-stranded DNA/RNA virus
Genome polyprotein / Genome polyprotein / Genome polyprotein
|Biological species||Deformed wing virus|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å|
|Authors||Skubnik, K. / Novacek, J. / Fuzik, T. / Pridal, A. / Paxton, R. / Plevka, P.|
|Funding support||2items |
|Citation||Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017|
Title: Structure of deformed wing virus, a major honey bee pathogen.
Authors: Karel Škubník / Jiří Nováček / Tibor Füzik / Antonín Přidal / Robert J Paxton / Pavel Plevka /
Abstract: The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) ...The worldwide population of western honey bees () is under pressure from habitat loss, environmental stress, and pathogens, particularly viruses that cause lethal epidemics. Deformed wing virus (DWV) from the family , together with its vector, the mite , is likely the major threat to the world's honey bees. However, lack of knowledge of the atomic structures of iflaviruses has hindered the development of effective treatments against them. Here, we present the virion structures of DWV determined to a resolution of 3.1 Å using cryo-electron microscopy and 3.8 Å by X-ray crystallography. The C-terminal extension of capsid protein VP3 folds into a globular protruding (P) domain, exposed on the virion surface. The P domain contains an Asp-His-Ser catalytic triad that is, together with five residues that are spatially close, conserved among iflaviruses. These residues may participate in receptor binding or provide the protease, lipase, or esterase activity required for entry of the virus into a host cell. Furthermore, nucleotides of the DWV RNA genome interact with VP3 subunits. The capsid protein residues involved in the RNA binding are conserved among honey bee iflaviruses, suggesting a putative role of the genome in stabilizing the virion or facilitating capsid assembly. Identifying the RNA-binding and putative catalytic sites within the DWV virion structure enables future analyses of how DWV and other iflaviruses infect insect cells and also opens up possibilities for the development of antiviral treatments.
SummaryFull reportAbout validation report
|Structure viewer||Molecule: |
Downloads & links
A: VP1x 60
A: VP1x 5
A: VP1x 6
|Symmetry||Point symmetry: (Schoenflies symbol: I (icosahedral))|
|#1: Protein|| |
Mass: 28679.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: L0CTV4
|#2: Protein|| |
Mass: 28360.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: E0YTW0, UniProt: Q7TG18*PLUS
|#3: Protein|| |
Mass: 46697.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Deformed wing virus / References: UniProt: Q7TG18
|#4: Chemical|| ChemComp-U5P / |
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|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 / Isolate: OTHER / Type: VIRION|
|Natural host||Organism: Apis mellifera|
|Virus shell||Diameter: 390 nm / Triangulation number (T number): 3|
|Buffer solution||pH: 7.4 |
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 was virus ...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 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 divisions/in. / Grid type: Quantifoil R2/1|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Calibrated magnification: 74235 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE|
|Specimen holder||Cryogen: NITROGEN / 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) / Num. of grids imaged: 1|
|Image scans||Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Particle selection||Num. of particles selected: 3918|
|3D reconstruction||Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 879 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT|
|Atomic model building||Protocol: OTHER / Space: REAL / Target criteria: R-factor|
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