National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
1RO1AI118933
United States
National Science Foundation (NSF, United States)
CBET 1803440
United States
Citation
Journal: Small / Year: 2020 Title: Virus Assembly Pathways: Straying Away but Not Too Far. Authors: Kevin Bond / Irina B Tsvetkova / Joseph Che-Yen Wang / Martin F Jarrold / Bogdan Dragnea / Abstract: Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate ...Non-enveloped RNA viruses pervade all domains of life. In a cell, they co-assemble from viral RNA and capsid proteins. Virus-like particles can form in vitro where virtually any non-cognate polyanionic cargo can be packaged. How only viral RNA gets selected for packaging in vivo, in presence of myriad other polyanionic species, has been a puzzle. Through a combination of charge detection mass spectrometry and cryo-electron microscopy, it is determined that co-assembling brome mosaic virus (BMV) coat proteins and nucleic acid oligomers results in capsid structures and stoichiometries that differ from the icosahedral virion. These previously unknown shell structures are strained and less stable than the native one. However, they contain large native structure fragments that can be recycled to form BMV virions, should a viral genome become available. The existence of such structures suggest the possibility of a previously unknown regulatory pathway for the packaging process inside cells.
History
Deposition
Sep 24, 2020
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Header (metadata) release
Dec 9, 2020
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Map release
Dec 9, 2020
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Update
Dec 30, 2020
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Current status
Dec 30, 2020
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_22709.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
BMV VLP assembled on PolyA with D6 symmetry
Voxel size
X=Y=Z: 0.843 Å
Density
Contour Level
By AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum
-0.013091089 - 0.019065376
Average (Standard dev.)
5.5686687e-05 (±0.0015208521)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
-200
-200
-200
Dimensions
400
400
400
Spacing
400
400
400
Cell
A=B=C: 337.2 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.843
0.843
0.843
M x/y/z
400
400
400
origin x/y/z
0.000
0.000
0.000
length x/y/z
337.200
337.200
337.200
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
-200
-200
-200
NC/NR/NS
400
400
400
D min/max/mean
-0.013
0.019
0.000
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Supplemental data
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Sample components
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Entire : Brome mosaic virus
Entire
Name: Brome mosaic virus
Components
Virus: Brome mosaic virus
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Supramolecule #1: Brome mosaic virus
Supramolecule
Name: Brome mosaic virus / type: virus / ID: 1 / Parent: 0 Details: The purified BMV was disassembled and the RNA precipitated. The capsid protein was then assembled with 52 nt of polyA. NCBI-ID: 12302 / Sci species name: Brome mosaic virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)
Organism: Nicotiana benthamiana (plant)
Molecular weight
Experimental: 2.5 MDa
Virus shell
Shell ID: 1 / Name: capsid / Diameter: 220.0 Å
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 4.5 / Component - Concentration: 100.0 mM / Component - Name: Ammonium acetate Details: 100 mM ammonium acetate that was pH adjusted to 4.5 with acetic acid
Grid
Model: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: 15 s blotting time, 0 blotting force, and 100% humidity in Mark IV..
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Electron microscopy
Microscope
FEI TALOS ARCTICA
Image recording
Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beam
Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron optics
C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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