+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12155 | |||||||||
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Title | KBV empty particle missing pentamer at acidic pH (C1) | |||||||||
Map data | KBV empty particle missing pentamer at acidic pH (C1) | |||||||||
Sample |
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Function / homology | Function and homology information | |||||||||
Biological species | Apis mellifera (honey bee) / Kashmir bee virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 21.0 Å | |||||||||
Authors | Mukhamedova L / Plevka P | |||||||||
Funding support | Czech Republic, 2 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12155.map.gz | 74.3 MB | EMDB map data format | |
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Header (meta data) | emd-12155-v30.xml emd-12155.xml | 14.4 KB 14.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12155_fsc.xml | 18.5 KB | Display | FSC data file |
Images | emd_12155.png | 144.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12155 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12155 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12155.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | KBV empty particle missing pentamer at acidic pH (C1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Kashmir bee virus
Entire | Name: Kashmir bee virus |
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Components |
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-Supramolecule #1: Kashmir bee virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: Apis mellifera (honey bee) |
Molecular weight | Theoretical: 5.932 MDa |
Virus shell | Shell ID: 1 / Name: Full virus / Diameter: 350.0 Å / T number (triangulation number): 3 |
-Macromolecule #1: Icosahedral virus
Macromolecule | Name: Icosahedral virus / type: other / ID: 1 / Classification: other |
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Source (natural) | Organism: Apis mellifera (honey bee) |
Sequence | String: NFKYLRCDVQ VKIVLNANPF IAGRLYLAYS PYDDKVAPER RIIYTSRAGV TGYPGVELDF QLDNSVEMTI PYASFQEAY DLVSGTEDFV QLYLFTITPV LGPSAESANS KVDLSVYMWL DNISLVIPTY RLNPNLPTGQ T LTRIVQNS DSDKLKEALK IAKSKNPSGY ...String: NFKYLRCDVQ VKIVLNANPF IAGRLYLAYS PYDDKVAPER RIIYTSRAGV TGYPGVELDF QLDNSVEMTI PYASFQEAY DLVSGTEDFV QLYLFTITPV LGPSAESANS KVDLSVYMWL DNISLVIPTY RLNPNLPTGQ T LTRIVQNS DSDKLKEALK IAKSKNPSGY KYIMGVLEQY NPSVKQVSMQ IATPNKSKST KPTSENPKIG PI SEVASGV KTAANGIERI PVLGEIAKPV TAAVKWFADI VGGVAAIFGW SKPRNQNQVM PYQNVPGWGY SLY KGIDMS VPLAYDPNNE LGDLRDVFPS AVDEMAIGYV CGNPAIKHVL TWNTTDAVQN PISNGDDWGG VIPV GMPCY SKTIRAVKGD TSTSKTEVMD PAPCEYVANL FSYWRATMCY RITVVKTAFH TGRLEIFFEP GSIPT VRTA DNLGPDQTQL NGTVAPSDNN YKYILDLTND TEVTIKVPYV SNKMFMKTVG IYGANDENNW DFDESF TGF LCIRPITKLM APDTVSQKVS IVVWKWAEDV VVVEPKPLTS GPTQVYNPPA VARDQVKQID VSMQINL SN KTDENTISFF DSGDPERMNS EALMRGCGEQ IVNLRPLLRT FRTINDNWSL AANTKTPITD LTNTADAE G RDYMSYLSFL YRFYRGGRRY KFFNTTPLKQ SQTCYVRSFL IPRNYTADEI NTDGPSHITY PVINPVHEV EVPFYSQYRK IPIASTTDKG YDSSLMYYTN VGTQQIVARA GNDDFTFGWM IGTPQLQGIT KEVAN |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: -0.004 µm / Calibrated defocus min: -0.0002 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: -0.0018000000000000002 µm / Nominal defocus min: -0.001 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 103.15 K / Max: 108.15 K |
Image recording | Film 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 27.78 / Target criteria: Cross- correlation |