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- PDB-7bg8: KBV activated particle at acidic pH -

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Basic information

Entry
Database: PDB / ID: 7bg8
TitleKBV activated particle at acidic pH
Components(Structural polyprotein) x 4
KeywordsVIRUS / Viruses / Riboviria / Orthornavirae / Pisuviricota / Pisoniviricetes / Picornavirales / Dicistroviridae / Aparavirus / 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 speciesKashmir bee virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsMukhamedova, L. / Plevka, P. / Fuzik, T. / Hrebik, D.
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 6, 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
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_volume / _citation_author.identifier_ORCID ..._citation.journal_volume / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jul 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / refine
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _refine.ls_d_res_high / _refine.ls_d_res_low

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)98,9604
Polymers98,9604
Non-polymers00
Water00
1
A: Structural polyprotein
C: Structural polyprotein
B: Structural polyprotein
D: Structural polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)5,937,570240
Polymers5,937,570240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation59

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Components

#1: 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
#2: 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
#3: 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
#4: 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

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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 virus / 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: 300 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 FIELD / Nominal magnification: 75000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 200 nm / Calibrated defocus min: 214 nm / Calibrated defocus max: 4134 nm / Cs: 2.7 mm / C2 aperture diameter: 50 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: 94 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8193
Image scansWidth: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: (1.18.2_3874: ???) / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
4Gctf1.6CTF correction
7PHENIX1.18.2model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
19PHENIX1.18.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 794 / Details: I4 symmetry implemented. / Symmetry type: POINT
Atomic model buildingB value: 45.18 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross- correlation
Atomic model buildingPDB-ID: 5CDC

5cdc


Accession code: 5CDC / Source name: PDB / Type: experimental model
RefinementResolution: 4→4 Å / SU ML: 0.87 / σ(F): 0.15 / Phase error: 48.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4266 1671 1.17 %
Rwork0.4018 --
obs0.4021 142224 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00728340
ELECTRON MICROSCOPYf_angle_d0.69538695
ELECTRON MICROSCOPYf_dihedral_angle_d17.07210280
ELECTRON MICROSCOPYf_chiral_restr0.0444330
ELECTRON MICROSCOPYf_plane_restr0.0044995
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.010.5711420.51511643ELECTRON MICROSCOPY100
4.01-4.140.52271380.470811587ELECTRON MICROSCOPY100
4.14-4.290.40471390.438711690ELECTRON MICROSCOPY100
4.29-4.460.52431330.419511639ELECTRON MICROSCOPY100
4.46-4.670.44631390.409811648ELECTRON MICROSCOPY100
4.67-4.910.3821370.402111679ELECTRON MICROSCOPY100
4.91-5.220.4341390.395311687ELECTRON MICROSCOPY100
5.22-5.620.41451380.391711703ELECTRON MICROSCOPY100
5.62-6.190.50681410.41811714ELECTRON MICROSCOPY100
6.19-7.090.45111420.410211763ELECTRON MICROSCOPY100
7.09-8.920.42961400.368211798ELECTRON MICROSCOPY100
8.93-96.590.30361430.327712002ELECTRON MICROSCOPY99

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