+Open data
-Basic information
Entry | Database: PDB / ID: 6f5j | |||||||||
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Title | Structure of deformed wing virus carrying the GFP gene | |||||||||
Components | (Genome polyprotein) x 3 | |||||||||
Keywords | VIRAL PROTEIN / Deformed wing virus / Picornavirales / Iflaviridae / Iflavirus | |||||||||
Function / homology | Function and homology information host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis ...host cell membrane / viral capsid / host cell cytoplasm / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Deformed wing virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||
Authors | Skubnik, K. / Plevka, P. | |||||||||
Funding support | 2items
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Citation | Journal: Curr Opin Virol / Year: 2020 Title: Virion structures and genome delivery of honeybee viruses. Authors: Michaela Procházková / Karel Škubník / Tibor Füzik / Liya Mukhamedova / Antonín Přidal / Pavel Plevka / Abstract: The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. ...The western honeybee is the primary pollinator of numerous food crops. Furthermore, honeybees are essential for ecosystem stability by sustaining the diversity and abundance of wild flowering plants. However, the worldwide population of honeybees is under pressure from environmental stress and pathogens. Viruses from the families Iflaviridae and Dicistroviridae, together with their vector, the parasitic mite Varroa destructor, are the major threat to the world's honeybees. Dicistroviruses and iflaviruses have capsids with icosahedral symmetries. Acidic pH triggers the genome release of both dicistroviruses and iflaviruses. The capsids of iflaviruses expand, whereas those of dicistroviruses remain compact until the genome release. Furthermore, dicistroviruses use inner capsid proteins, whereas iflaviruses employ protruding domains or minor capsid proteins from the virion surface to penetrate membranes and deliver their genomes into the cell cytoplasm. The structural characterization of the infection process opens up possibilities for the development of antiviral compounds. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6f5j.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f5j.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 6f5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f5j_validation.pdf.gz | 838.7 KB | Display | wwPDB validaton report |
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Full document | 6f5j_full_validation.pdf.gz | 845.6 KB | Display | |
Data in XML | 6f5j_validation.xml.gz | 40 KB | Display | |
Data in CIF | 6f5j_validation.cif.gz | 59.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/6f5j ftp://data.pdbj.org/pub/pdb/validation_reports/f5/6f5j | HTTPS FTP |
-Related structure data
Related structure data | 4189MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#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 |
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#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 |
#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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Deformed wing virus / Type: VIRUS / Details: Virus was purified from honeybee pupae. / Entity ID: all / Source: NATURAL |
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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 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Virus was dissolved in PBS buffer. |
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
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | 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 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 |
Image scans | Width: 4096 / Height: 4096 / Movie frames/image: 16 / Used frames/image: 2-16 |
-Processing
Software | Name: PHENIX / Version: (1.12rc0_2787: ???) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 32573 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21000 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 3.1→243.399 Å / SU ML: 0.8 / σ(F): 0.04 / Phase error: 48.02 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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