National Health and Medical Research Council (NHMRC, Australia)
APP1164216
Australia
Citation
Journal: Nat Commun / Year: 2021 Title: A unified route for flavivirus structures uncovers essential pocket factors conserved across pathogenic viruses. Authors: Joshua M Hardy / Natalee D Newton / Naphak Modhiran / Connor A P Scott / Hariprasad Venugopal / Laura J Vet / Paul R Young / Roy A Hall / Jody Hobson-Peters / Fasséli Coulibaly / Daniel Watterson / Abstract: The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat ...The epidemic emergence of relatively rare and geographically isolated flaviviruses adds to the ongoing disease burden of viruses such as dengue. Structural analysis is key to understand and combat these pathogens. Here, we present a chimeric platform based on an insect-specific flavivirus for the safe and rapid structural analysis of pathogenic viruses. We use this approach to resolve the architecture of two neurotropic viruses and a structure of dengue virus at 2.5 Å, the highest resolution for an enveloped virion. These reconstructions allow improved modelling of the stem region of the envelope protein, revealing two lipid-like ligands within highly conserved pockets. We show that these sites are essential for viral growth and important for viral maturation. These findings define a hallmark of flavivirus virions and a potential target for broad-spectrum antivirals and vaccine design. We anticipate the chimeric platform to be widely applicable for investigating flavivirus biology.
History
Deposition
Nov 27, 2020
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Header (metadata) release
Dec 23, 2020
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Map release
Dec 23, 2020
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Update
Jul 14, 2021
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Current status
Jul 14, 2021
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Name: Kunjin virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: Virus amplified in Aedes albopictus C6/36 cells. M and E from West Nile virus (Kunjin) form a complex that assembles into anti-parallel dimers, (M-E)2, in the T=3 icosahedral particle. NCBI-ID: 11077 / Sci species name: Kunjin virus / Sci species strain: NSW2011 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)
Organism: Culex annulirostris (mosquito)
Molecular weight
Theoretical: 22 MDa
Virus shell
Shell ID: 1 / Diameter: 470.0 Å / T number (triangulation number): 3
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Macromolecule #1: Envelope protein E
Macromolecule
Name: Envelope protein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 0 second wait time 2 second blot time -10 blot force 1 second drain time.
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1517 / Average exposure time: 12.8 sec. / Average electron dose: 57.6 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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