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

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Basic information

Entry
Database: PDB / ID: 7bgk
TitleNative virion of Kashmir bee virus at neutral pH
Components(Structural polyprotein) x 4
KeywordsVIRUS / Viruses / Riboviria / Orthornavirae / Pisuviricota / Pisoniviricetes / Picornavirales / Dicistroviridae / Aparavirus / Kashmir Bee 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 / Structural polyprotein
Similarity search - Component
Biological speciesKashmir bee virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMukhamedova, L. / Plevka, P. / Fuzik, T. / Hrebik, D. / Novacek, J.
Funding support Czech Republic, 2items
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 30, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_volume / _citation_author.identifier_ORCID ..._citation.journal_volume / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
D: Structural polyprotein
A: Structural polyprotein
C: Structural polyprotein
B: Structural polyprotein


Theoretical massNumber of molelcules
Total (without water)98,9604
Polymers98,9604
Non-polymers00
Water0
1
D: Structural polyprotein
A: Structural polyprotein
C: Structural polyprotein
B: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)5,937,570240
Polymers5,937,570240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Structural polyprotein


Mass: 7066.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kashmir bee virus / References: UniProt: Q6SQI6
#2: Protein Structural polyprotein


Mass: 23807.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kashmir bee virus / References: UniProt: Q80AG2
#3: Protein Structural polyprotein


Mass: 33335.781 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kashmir bee virus / References: UniProt: Q80AG2
#4: Protein Structural polyprotein


Mass: 34750.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Kashmir bee virus / References: UniProt: Q80AG2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: TISSUE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Kashmir bee virusList of diseases of the honey bee / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 5.932 MDa / Experimental value: NO
Source (natural)Organism: Kashmir bee virus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Apis mellifera
Virus shellName: Full virus / Diameter: 350 nm / Triangulation number (T number): 3
Buffer solutionpH: 6
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 620 nm / Calibrated defocus max: 3627 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 108.15 K / Temperature (min): 103.15 K
Image recordingAverage exposure time: 1 sec. / Electron dose: 54 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1
Image scansWidth: 4096 / Height: 4096 / Movie frames/image: 7

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.6CTF correction
7PHENIX1.18.2model fitting
9PHENIX1.18.2model refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 466310 / Symmetry type: POINT
Atomic model buildingB value: 27.78 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross- correlation
Atomic model buildingPDB-ID: 5CDC

5cdc

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00864100
ELECTRON MICROSCOPYf_angle_d1.346115830
ELECTRON MICROSCOPYf_dihedral_angle_d9.09725925
ELECTRON MICROSCOPYf_chiral_restr0.095040
ELECTRON MICROSCOPYf_plane_restr0.0049565

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