Journal: J Virol / Year: 2007 Title: Structure of immature West Nile virus. Authors: Ying Zhang / Bärbel Kaufmann / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Abstract: The structure of immature West Nile virus particles, propagated in the presence of ammonium chloride to block virus maturation in the low-pH environment of the trans-Golgi network, was determined by ...The structure of immature West Nile virus particles, propagated in the presence of ammonium chloride to block virus maturation in the low-pH environment of the trans-Golgi network, was determined by cryo-electron microscopy (cryo-EM). The structure of these particles was similar to that of immature West Nile virus particles found as a minor component of mature virus samples (naturally occurring immature particles [NOIPs]). The structures of mature infectious flaviviruses are radically different from those of the immature particles. The similarity of the ammonium chloride-treated particles and NOIPs suggests either that the NOIPs have not undergone any conformational change during maturation or that the conformational change is reversible. Comparison with the cryo-EM reconstruction of immature dengue virus established the locations of the N-linked glycosylation sites of these viruses, verifying the interpretation of the reconstructions of the immature flaviviruses.
History
Deposition
Jan 2, 2007
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Header (metadata) release
Jan 2, 2007
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Map release
Jun 11, 2007
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Update
Oct 24, 2012
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Current status
Oct 24, 2012
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Cryogen name: ETHANE Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
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Electron microscopy
Microscope
FEI/PHILIPS CM300FEG/T
Temperature
Average: 98 K
Alignment procedure
Legacy - Astigmatism: live FFT at 200K mag
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Number real images: 45 / Average electron dose: 22 e/Å2
Tilt angle min
0
Tilt angle max
0
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFTSEARCH, OOR, P3DR Details: magnification of final map standardized to a map calculated from immature dengue virus Number images used: 341
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