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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12173 | |||||||||
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Title | KBV activated particle at acidic pH | |||||||||
![]() | KBV activated particle at acidic pH | |||||||||
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![]() | Viruses / Riboviria / Orthornavirae / Pisuviricota / Pisoniviricetes / Picornavirales / Dicistroviridae / Aparavirus / Kashmir Bee Virus / VIRUS | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.0 Å | |||||||||
![]() | Mukhamedova L / Plevka P | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 67.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.7 KB 18.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 18.1 KB | Display | ![]() |
Images | ![]() | 303.2 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7bg8MC ![]() 7bc3C ![]() 7be9C ![]() 7bgkC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | KBV activated particle at acidic pH | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
-Entire : Kashmir bee virus
Entire | Name: ![]() |
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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: ![]() ![]() |
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: Structural polyprotein
Macromolecule | Name: Structural polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 23.807529 KDa |
Sequence | String: 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 UniProtKB: Structural polyprotein |
-Macromolecule #2: Structural polyprotein
Macromolecule | Name: Structural polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 33.335781 KDa |
Sequence | String: 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 UniProtKB: Structural polyprotein |
-Macromolecule #3: Structural polyprotein
Macromolecule | Name: Structural polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 34.750039 KDa |
Sequence | String: 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 UniProtKB: Structural polyprotein |
-Macromolecule #4: Structural polyprotein
Macromolecule | Name: Structural polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.066156 KDa |
Sequence | String: IATPNKSKST KPTSENPKIG PISEVASGVK TAANGIERIP VLGEIAKPVT AAVKWFADIV GGVAAIFGW UniProtKB: Structural polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | tissue |
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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |