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- EMDB-12154: Kashmir bee virus empty particle at acidic pH -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-12154
TitleKashmir bee virus empty particle at acidic pH
Map dataKBV empty particle at acidic pH
Sample
  • Virus: Kashmir bee virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
KeywordsViruses / Riboviria / Orthornavirae / Pisuviricota / Pisoniviricetes / Picornavirales / Dicistroviridae / Aparavirus / Kashmir Bee Virus / VIRUS
Function / homology
Function and homology information


viral capsid / 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
Similarity search - Component
Biological speciesKashmir bee virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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 6, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7be9
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7be9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12154.png

Downloads & links

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Map

FileDownload / File: emd_12154.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKBV empty particle 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: 0.013 / Movie #1: 0.013
Minimum - Maximum-0.03555359 - 0.04846256
Average (Standard dev.)0.00039164687 (±0.005160185)
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-0.0360.0480.000

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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
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein

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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: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 22.735377 KDa
SequenceString: ENTISFFDSG DPERMNNEAL MRGCGEQIVN LRPLLRTFRT INDNWSLAAN TKTPITDLTN TADAEGRDYM SYLSFLYRFY RGGRRYKFF NTTPLKQSQT CYVRSFLIPR NYTADEINTD GPSHITYPVI NPVHEVEVPF YSQYRKIPIA STSDKGYDSS L MYYTNVGT ...String:
ENTISFFDSG DPERMNNEAL MRGCGEQIVN LRPLLRTFRT INDNWSLAAN TKTPITDLTN TADAEGRDYM SYLSFLYRFY RGGRRYKFF NTTPLKQSQT CYVRSFLIPR NYTADEINTD GPSHITYPVI NPVHEVEVPF YSQYRKIPIA STSDKGYDSS L MYYTNVGT QQIVARAGND DFTFGWMIGT PQLQGITKEV

UniProtKB: Structural polyprotein

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Macromolecule #2: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 31.920127 KDa
SequenceString: SKPRNQNQVM PYQNVPGWGY SLYKGIDMSV PLAYDPNNEL GDLRDVFPSA VDEMAIGYVC GNPAIKHVLT WSTTDVVQNP ISNGDDWGG VIPVGMPCYS KTIRAVKGAT STSKTEVMDP APCEYVANLF SYWRATMCYR ITVVKTAFHT GRLEIFFEPG S IPTVRTAD ...String:
SKPRNQNQVM PYQNVPGWGY SLYKGIDMSV PLAYDPNNEL GDLRDVFPSA VDEMAIGYVC GNPAIKHVLT WSTTDVVQNP ISNGDDWGG VIPVGMPCYS KTIRAVKGAT STSKTEVMDP APCEYVANLF SYWRATMCYR ITVVKTAFHT GRLEIFFEPG S IPTVRTAD NLGPDQTQLN GTIAPSDNNY KYILDLTNDT EVTIKVPYVS NKMFMKTVGI YGAHDEDNWN FDESFTGFLC IR PITKLMA PDTVSQKVSI VVWKWAEDVV VVEPKPLTSG PTQVYNPPAV A

UniProtKB: Structural polyprotein

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Macromolecule #3: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 21.998068 KDa
SequenceString: SIIQFLQRPV LIDNIEIVAG TTADNNTALS RYVLDRTNPQ KYIKQWTLPS TVLKAGGKAQ KLANFKYLRC DVQVKIVLNA NPFIAGRLY LAYSPYDDKV APERRIIYTS RAGVTGYPGV ELDFQLDNSV EMTIPYASFQ EAYDLVSGNE DFVQLYLFTI A PVLGPSAE ...String:
SIIQFLQRPV LIDNIEIVAG TTADNNTALS RYVLDRTNPQ KYIKQWTLPS TVLKAGGKAQ KLANFKYLRC DVQVKIVLNA NPFIAGRLY LAYSPYDDKV APERRIIYTS RAGVTGYPGV ELDFQLDNSV EMTIPYASFQ EAYDLVSGNE DFVQLYLFTI A PVLGPSAE SANSKVDLSV YMWLDNISLV IPTYRLNP

UniProtKB: Structural polyprotein

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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 / Support film - Material: CARBON / Support film - topology: HOLEY
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: 4.134 µm / Calibrated defocus min: 0.214 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.2 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 reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 2366
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


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 61.48 / Target criteria: Cross- correlation
Output model

PDB-7be9:
Kashmir bee virus empty particle at acidic pH

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