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- EMDB-12182: Native virion of Kashmir bee virus at neutral pH -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-12182
TitleNative virion of Kashmir bee virus at neutral pH
Map dataKBV native virion at neutral pH
Sample
  • Virus: Kashmir bee virus
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
    • Protein or peptide: Structural polyprotein
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 speciesKashmir bee virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMukhamedova L / Plevka P / Fuzik T / Hrebik D / Novacek J
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 7, 2021-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateNov 30, 2022-
Current statusNov 30, 2022Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bgk
  • Surface level: 1.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bgk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12182.png

Downloads & links

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Map

FileDownload / File: emd_12182.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKBV native virion at neutral pH
Voxel sizeX=Y=Z: 1.063 Å
Density
Contour LevelBy AUTHOR: 1.7 / Movie #1: 1.7
Minimum - Maximum-9.535916 - 14.242681
Average (Standard dev.)-1.5076709e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-170-170-170
Dimensions340340340
Spacing340340340
CellA=B=C: 361.41998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z361.420361.420361.420
α/β/γ90.00090.00090.000
start NX/NY/NZ-170-170-170
NX/NY/NZ340340340
MAP C/R/S312
start NC/NR/NS-170-170-170
NC/NR/NS340340340
D min/max/mean-9.53614.243-0.000

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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
    • 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: 7.066156 KDa
SequenceString:
IATPNKSKST KPTSENPKIG PISEVASGVK TAANGIERIP VLGEIAKPVT AAVKWFADIV GGVAAIFGW

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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: 23.807529 KDa
SequenceString: INLSNKTDEN TISFFDSGDP ERMNNEALMR GCGEQIVNLR PLLRTFRTIN DNWSLAANTK TPITDLTNTA DAEGRDYMSY LSFLYRFYR GGRRYKFFNT TPLKQSQTCY VRSFLIPRNY TADEINTDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL ...String:
INLSNKTDEN TISFFDSGDP ERMNNEALMR GCGEQIVNLR PLLRTFRTIN DNWSLAANTK TPITDLTNTA DAEGRDYMSY LSFLYRFYR GGRRYKFFNT TPLKQSQTCY VRSFLIPRNY TADEINTDGP SHITYPVINP VHEVEVPFYS QYRKIPIAST S DKGYDSSL MYYTNVGTQQ IVARAGNDDF TFGWMIGTPQ LQGITKEVAN

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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: 33.335781 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 ARDLVKQIDV SMQ

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Macromolecule #4: Structural polyprotein

MacromoleculeName: Structural polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Kashmir bee virus
Molecular weightTheoretical: 34.750039 KDa
SequenceString: ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVAG TTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN ANPFIAGRLY LAYSPYDDKV A PERRIIYT ...String:
ADNQENDSTN VHNTKLASTS AENAIEKEQI TTFHDVETPN RIDTPMAQDT SSARSMDDTH SIIQFLQRPV LIDNIEIVAG TTADNNTAL SRYVLDRTNP QKYIKQWTLP STVLKAGGKA QKLANFKYLR CDVQVKIVLN ANPFIAGRLY LAYSPYDDKV A PERRIIYT SRAGVTGYPG VELDFQLDNS VEMTIPYASF QEAYDLVSGN EDFVQLYLFT IAPVLGPSAE SANSKVDLSV YM WLDNISL VIPTYRLNPN LPTGQTLTRI VQNSDSDKLK EALKIAKSKN PSGYKYIMGV LEQYNPSVKQ VSMQ

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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: 200 / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.6270000000000002 µm / Calibrated defocus min: 0.62 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 103.15 K / Max: 108.15 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4115

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 466310
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
Output model

PDB-7bgk:
Native virion of Kashmir bee virus at neutral pH

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