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- EMDB-11716: Open empty capsid of SBPV in acidic pH -

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Basic information

Entry
Database: EMDB / ID: EMD-11716
TitleOpen empty capsid of SBPV in acidic pH
Map data
Sample
  • Virus: Slow bee paralysis virus
Biological speciesSlow bee paralysis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 26.0 Å
AuthorsSkubnik K / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
CitationJournal: Sci Adv / Year: 2021
Title: Capsid opening enables genome release of iflaviruses.
Authors: Karel Škubník / Lukáš Sukeník / David Buchta / Tibor Füzik / Michaela Procházková / Jana Moravcová / Lenka Šmerdová / Antonín Přidal / Robert Vácha / Pavel Plevka /
Abstract: The family Iflaviridae includes economically important viruses of the western honeybee such as deformed wing virus, slow bee paralysis virus, and sacbrood virus. Iflaviruses have nonenveloped virions ...The family Iflaviridae includes economically important viruses of the western honeybee such as deformed wing virus, slow bee paralysis virus, and sacbrood virus. Iflaviruses have nonenveloped virions and capsids organized with icosahedral symmetry. The genome release of iflaviruses can be induced in vitro by exposure to acidic pH, implying that they enter cells by endocytosis. Genome release intermediates of iflaviruses have not been structurally characterized. Here, we show that conformational changes and expansion of iflavirus RNA genomes, which are induced by acidic pH, trigger the opening of iflavirus particles. Capsids of slow bee paralysis virus and sacbrood virus crack into pieces. In contrast, capsids of deformed wing virus are more flexible and open like flowers to release their genomes. The large openings in iflavirus particles enable the fast exit of genomes from capsids, which decreases the probability of genome degradation by the RNases present in endosomes.
History
DepositionSep 10, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00777
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00777
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11716.png

Downloads & links

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Map

FileDownload / File: emd_11716.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 544.256 Å		1.06 Å/pix.
x 512 pix.
= 544.256 Å		1.06 Å/pix.
x 512 pix.
= 544.256 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00777 / Movie #1: 0.00777
Minimum - Maximum-0.010523453 - 0.02009706
Average (Standard dev.)0.00024099177 (±0.0024969873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 544.256 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z544.256544.256544.256
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0110.0200.000

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Supplemental data

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Half map: #1

Fileemd_11716_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11716_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Slow bee paralysis virus

EntireName: Slow bee paralysis virus
Components
  • Virus: Slow bee paralysis virus

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Supramolecule #1: Slow bee paralysis virus

SupramoleculeName: Slow bee paralysis virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 458132 / Sci species name: Slow bee paralysis virus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)

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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: 5.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3574

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1737
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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