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- EMDB-11714: Open empty capsid of SBV in acidic pH -

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Basic information

Entry
Database: EMDB / ID: EMD-11714
TitleOpen empty capsid of SBV in acidic pH
Map data
Sample
  • Virus: Sacbrood virus
Biological speciesSacbrood virus
Methodsingle particle reconstruction / cryo EM / Resolution: 16.0 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: 0.0139
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0139
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11714.png

Downloads & links

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Map

FileDownload / File: emd_11714.map.gz / Format: CCP4 / Size: 620.9 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 546 pix.
= 580.398 Å		1.06 Å/pix.
x 546 pix.
= 580.398 Å		1.06 Å/pix.
x 546 pix.
= 580.398 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: 0.0139 / Movie #1: 0.0139
Minimum - Maximum-0.014561846 - 0.030121561
Average (Standard dev.)0.0003708617 (±0.0041312324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions546546546
Spacing546546546
CellA=B=C: 580.398 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z546546546
origin x/y/z0.0000.0000.000
length x/y/z580.398580.398580.398
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS546546546
D min/max/mean-0.0150.0300.000

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Supplemental data

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Half map: #1

Fileemd_11714_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_11714_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 : Sacbrood virus

EntireName: Sacbrood virus
Components
  • Virus: Sacbrood virus

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Supramolecule #1: Sacbrood virus

SupramoleculeName: Sacbrood virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 89463 / Sci species name: Sacbrood 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 reconstructionResolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7549
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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