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- EMDB-12168: KBV empty particle with bulging pentamer at acidic pH -

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Basic information

Entry
Database: EMDB / ID: EMD-12168
TitleKBV empty particle with bulging pentamer at acidic pH
Map dataKBV empty particle with bulging pentamer at acidic pH
Sample
  • Virus: Kashmir bee virus
    • Other: Kashmir bee virus
Function / homology
Function and homology information


structural molecule activity
Similarity search - Function
Capsid protein VP4, dicistrovirus / Cricket paralysis virus, VP4 / Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Structural polyprotein / Structural polyprotein
Similarity search - Component
Biological speciesApis mellifera (honey bee) / Kashmir bee virus
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsMukhamedova L / Plevka P
Funding support Czech Republic, 2 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
Ministry of Education (MoE, Czech Republic)LM2011033 Czech Republic
CitationJournal: J Virol / Year: 2021
Title: Virion structure and genome release mechanism of dicistrovirus Kashmir bee virus.
Authors: Liya Mukhamedova / Tibor Füzik / Jiří Nováček / Dominik Hrebík / Antonín Přidal / Gerardo A Marti / Diego M A Guérin / Pavel Plevka /
Abstract: Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number ...Infections of Kashmir bee virus (KBV) are lethal for honeybees and have been associated with colony collapse disorder. KBV and closely related viruses contribute to the ongoing decline in the number of honeybee colonies in North America, Europe, Australia, and other parts of the world. Despite the economic and ecological impact of KBV, its structure and infection process remain unknown. Here we present the structure of the virion of KBV determined to a resolution of 2.8 Å. We show that the exposure of KBV to acidic pH induces a reduction in inter-pentamer contacts within capsids and the reorganization of its RNA genome from a uniform distribution to regions of high and low density. Capsids of KBV crack into pieces at acidic pH, resulting in the formation of open particles lacking pentamers of capsid proteins. The large openings of capsids enable the rapid release of genomes and thus limit the probability of their degradation by RNases. The opening of capsids may be a shared mechanism for the genome release of viruses from the family The western honeybee () is indispensable for maintaining agricultural productivity as well as the abundance and diversity of wild flowering plants. However, bees suffer from environmental pollution, parasites, and pathogens, including viruses. Outbreaks of virus infections cause the deaths of individual honeybees as well as collapses of whole colonies. Kashmir bee virus has been associated with colony collapse disorder in the US, and no cure of the disease is currently available. Here we report the structure of an infectious particle of Kashmir bee virus and show how its protein capsid opens to release the genome. Our structural characterization of the infection process determined that therapeutic compounds stabilizing contacts between pentamers of capsid proteins could prevent the genome release of the virus.
History
DepositionJan 5, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateDec 7, 2022-
Current statusDec 7, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12168.png

Downloads & links

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Map

FileDownload / File: emd_12168.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKBV empty particle with bulging pentamer at acidic pH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 340 pix.
= 363.8 Å		1.07 Å/pix.
x 340 pix.
= 363.8 Å		1.07 Å/pix.
x 340 pix.
= 363.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0055 / Movie #1: 0.0055
Minimum - Maximum-0.021806797 - 0.01815286
Average (Standard dev.)0.00057996664 (±0.003100346)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-170-170-170
Dimensions340340340
Spacing340340340
CellA=B=C: 363.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z363.800363.800363.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-170-170-170
NC/NR/NS340340340
D min/max/mean-0.0220.0180.001

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Supplemental data

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Sample components

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Entire : Kashmir bee virus

EntireName: Kashmir bee virus
Components
  • Virus: Kashmir bee virus
    • Other: Kashmir bee virus

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Supramolecule #1: Kashmir bee virus

SupramoleculeName: Kashmir bee virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 68876 / Sci species name: Kashmir bee virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Apis mellifera (honey bee)
Molecular weightTheoretical: 5.932 MDa
Virus shellShell ID: 1 / Name: Full virus / Diameter: 350.0 Å / T number (triangulation number): 3

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Macromolecule #1: Kashmir bee virus

MacromoleculeName: Kashmir bee virus / type: other / ID: 1 / Classification: other
Source (natural)Organism: Apis mellifera (honey bee)
SequenceString: ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVA GTTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN A NPFIAGRL YLAYSPYDDK VAPERRIIYT ...String:
ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVA GTTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN A NPFIAGRL YLAYSPYDDK VAPERRIIYT SRAGVTGYPG VELDFQLDNS VEMTIPYASF QEAYDLVSGN ED FVQLYLF TIAPVLGPSA ESANSKVDLS VYMWLDNISL VIPTYRLNPN LPTGQTLTRI VQNSDSDKLK EAL KIAKSK NPSGYKYIMG VLEQYNPSVK QVSMQIATPN KSKSTKPTSE NPKIGPISEV ASGVKTAANG IERI PVLGE IAKPVTAAVK WFADIVGGVA AIFGWSKPRN QNQVMPYQNV PGWGYSLYKG IDMSVPLAYD PNNEL GDLR DVFPSAVDEM AIGYVCGNPA IKHVLTWSTT DVVQNPISNG DDWGGVIPVG MPCYSKTIRA VKGATS TSK TEVMDPAPCE YVANLFSYWR ATMCYRITVV KTAFHTGRLE IFFEPGSIPT VRTADNLGPD QTQLNGT IA PSDNNYKYIL DLTNDTEVTI KVPYVSNKMF MKTVGIYGAH DEDNWNFDES FTGFLCIRPI TKLMAPDT V SQKVSIVVWK WAEDVVVVEP KPLTSGPTQV YNPPAVARDL VKQIDVSMQI NLSNKTDENT ISFFDSGDP ERMNNEALMR GCGEQIVNLR PLLRTFRTIN DNWSLAANTK TPITDLTNTA DAEGRDYMSY LSFLYRFYRG GRRYKFFNT TPLKQSQTCY VRSFLIPRNY TADEINTDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL MYYTNVGTQQ IVARAGNDDF TFGWMIGTPQ LQGITKEVAN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 103.15 K / Max: 108.15 K
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Number real images: 8193 / Average exposure time: 1.0 sec. / Average electron dose: 94.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: -0.004 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 75000
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

Startup modelType of model: EMDB MAP
EMDB ID:

4115

Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 14508
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5cdc

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 27.78 / Target criteria: Cross- correlation

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