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- EMDB-8464: Deformed Wing Virus 80-S Like Particle -

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Basic information

Entry
Database: EMDB / ID: EMD-8464
TitleDeformed Wing Virus 80-S Like Particle
Map dataDeformed Wing Virus 80-S Like Particle
Sample
  • Virus: Deformed wing virus
Biological speciesDeformed wing virus
Methodsingle particle reconstruction / Resolution: 6.1 Å
AuthorsOrgantini LJ / Hafenstein S / Conway JF / Makhov AM / Dryden KA / Pizzorno MC
CitationJournal: J Virol / Year: 2017
Title: Honey Bee Deformed Wing Virus Structures Reveal that Conformational Changes Accompany Genome Release.
Authors: Lindsey J Organtini / Kristin L Shingler / Robert E Ashley / Elizabeth A Capaldi / Kulsoom Durrani / Kelly A Dryden / Alexander M Makhov / James F Conway / Marie C Pizzorno / Susan Hafenstein /
Abstract: The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and ...The picornavirus-like deformed wing virus (DWV) has been directly linked to colony collapse; however, little is known about the mechanisms of host attachment or entry for DWV or its molecular and structural details. Here we report the three-dimensional (3-D) structures of DWV capsids isolated from infected honey bees, including the immature procapsid, the genome-filled virion, the putative entry intermediate (A-particle), and the empty capsid that remains after genome release. The capsids are decorated by large spikes around the 5-fold vertices. The 5-fold spikes had an open flower-like conformation for the procapsid and genome-filled capsids, whereas the putative A-particle and empty capsids that had released the genome had a closed tube-like spike conformation. Between the two conformations, the spikes undergo a significant hinge-like movement that we predicted using a Robetta model of the structure comprising the spike. We conclude that the spike structures likely serve a function during host entry, changing conformation to release the genome, and that the genome may escape from a 5-fold vertex to initiate infection. Finally, the structures illustrate that, similarly to picornaviruses, DWV forms alternate particle conformations implicated in assembly, host attachment, and RNA release.
IMPORTANCE: Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ...IMPORTANCE: Honey bees are critical for global agriculture, but dramatic losses of entire hives have been reported in numerous countries since 2006. Deformed wing virus (DWV) and infestation with the ectoparasitic mite Varroa destructor have been linked to colony collapse disorder. DWV was purified from infected adult worker bees to pursue biochemical and structural studies that allowed the first glimpse into the conformational changes that may be required during transmission and genome release for DWV.
History
DepositionNov 1, 2016-
Header (metadata) releaseNov 9, 2016-
Map releaseNov 9, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8464.png

Downloads & links

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Map

FileDownload / File: emd_8464.map.gz / Format: CCP4 / Size: 151.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeformed Wing Virus 80-S Like Particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 341 pix.
= 467.17 Å		1.37 Å/pix.
x 341 pix.
= 467.17 Å		1.37 Å/pix.
x 341 pix.
= 467.17 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1. / Movie #1: 1
Minimum - Maximum-5.8029914 - 6.3214893
Average (Standard dev.)0.000000001441012 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions341341341
Spacing341341341
CellA=B=C: 467.17 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z341341341
origin x/y/z0.0000.0000.000
length x/y/z467.170467.170467.170
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS341341341
D min/max/mean-5.8036.3210.000

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Supplemental data

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Sample components

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Entire : Deformed wing virus

EntireName: Deformed wing virus
Components
  • Virus: Deformed wing virus

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Supramolecule #1: Deformed wing virus

SupramoleculeName: Deformed wing virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 198112 / Sci species name: Deformed wing virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Apis mellifera (honey bee)
Virus shellShell ID: 1 / Name: VP1-4 / Diameter: 30.0 Å

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 5

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79958

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