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- EMDB-22708: BMV VLP assembled on oligoB with D5 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-22708
TitleBMV VLP assembled on oligoB with D5 symmetry
Map dataBMV VLP assembled on oligonucleotides with D5 symmetry
Sample
  • Virus: Brome mosaic virus
Biological speciesBrome mosaic virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsBond KM / Tsvetkova IB / Wang JC-Y / Jarrold MF / Dragnea B
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W911NF-17-1-0329 United States
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
CitationJournal: 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
DepositionSep 24, 2020-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22708.png

Downloads & links

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Map

FileDownload / File: emd_22708.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBMV VLP assembled on oligonucleotides with D5 symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.68 Å/pix.
x 256 pix.
= 430.08 Å		1.68 Å/pix.
x 256 pix.
= 430.08 Å		1.68 Å/pix.
x 256 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.037047498 - 0.060570963
Average (Standard dev.)0.00030027618 (±0.0030927097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-127-127-127
Dimensions256256256
Spacing256256256
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.681.681.68
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-127-127-127
NC/NR/NS256256256
D min/max/mean-0.0370.0610.000

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Supplemental data

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Sample components

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Entire : Brome mosaic virus

EntireName: Brome mosaic virus
Components
  • Virus: Brome mosaic virus

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Supramolecule #1: Brome mosaic virus

SupramoleculeName: 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 from a T-like region of the BMV RNA.
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 weightExperimental: 3.4 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 265.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 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
GridModel: C-flat / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: The initial model was built de novo using the SGD algorithm implemented in Relion 3.0.8 with C1 symmetry
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.8) / Number images used: 35621
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.08)

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