|Entry||Database: PDB / ID: 5mv6|
|Title||Structure of deformed wing virus, a honeybee pathogen|
|Keywords||VIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus|
|Function / homology|
Function and homology information
host cell membrane / RNA-protein covalent cross-linking / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / host cell cytoplasm / structural molecule activity / RNA binding ...host cell membrane / RNA-protein covalent cross-linking / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / host cell cytoplasm / structural molecule activity / RNA binding / membrane / ATP binding / cytoplasm
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / picornavirus capsid protein / Picornavirus capsid / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus ...Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / picornavirus capsid protein / Picornavirus capsid / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, catalytic domain / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / URIDINE-5'-MONOPHOSPHATE / Genome polyprotein / Genome polyprotein
Similarity search - Component
|Biological species||Deformed wing virus|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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.
|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-U / |
|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-#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: 5 |
Details: Dulbeccos Phosphate Buffered Saline D8537 sigma aldrich
|Specimen||Conc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Virus was incubated in PBS for 20 minutes at 34C.|
|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 / 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) / Num. of grids imaged: 1 / Num. of real images: 3000|
|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: 995|
|3D reconstruction||Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 945 / 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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