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- EMDB-28607: Acheta domesticus segmented densovirus VP-ORF1 virus-like particle -
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Open data
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Basic information
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Title | Acheta domesticus segmented densovirus VP-ORF1 virus-like particle | ||||||||||||
![]() | Acheta domesticus segmented densovirus VP-ORF1 virus-like particle | ||||||||||||
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![]() | parvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus / VIRUS LIKE PARTICLE | ||||||||||||
Function / homology | Capsid protein![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
![]() | Penzes JJ / McKenna R / Tijssen P | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Bipartite genome and structural organization of the parvovirus Acheta domesticus segmented densovirus. Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Emmanuel W Smith / Robert McKenna / Peter Tijssen / ![]() ![]() Abstract: Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression ...Parvoviruses (family Parvoviridae) are currently defined by a linear monopartite ssDNA genome, T = 1 icosahedral capsids, and distinct structural (VP) and non-structural (NS) protein expression cassettes within their genome. We report the discovery of a parvovirus with a bipartite genome, Acheta domesticus segmented densovirus (AdSDV), isolated from house crickets (Acheta domesticus), in which it is pathogenic. We found that the AdSDV harbors its NS and VP cassettes on two separate genome segments. Its vp segment acquired a phospholipase A2-encoding gene, vpORF3, via inter-subfamily recombination, coding for a non-structural protein. We showed that the AdSDV evolved a highly complex transcription profile in response to its multipartite replication strategy compared to its monopartite ancestors. Our structural and molecular examinations revealed that the AdSDV packages one genome segment per particle. The cryo-EM structures of two empty- and one full-capsid population (3.3, 3.1 and 2.3 Å resolution) reveal a genome packaging mechanism, which involves an elongated C-terminal tail of the VP, "pinning" the ssDNA genome to the capsid interior at the twofold symmetry axis. This mechanism fundamentally differs from the capsid-DNA interactions previously seen in parvoviruses. This study provides new insights on the mechanism behind ssDNA genome segmentation and on the plasticity of parvovirus biology. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 69.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.9 KB 12.9 KB | Display Display | ![]() |
Images | ![]() | 216.9 KB | ||
Filedesc metadata | ![]() | 6.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 544.8 KB | Display | ![]() |
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Full document | ![]() | 544.3 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 8.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8eu7MC ![]() 8er8C ![]() 8erkC ![]() 8eu6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Acheta domesticus segmented densovirus VP-ORF1 virus-like particle | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.049 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : unclassified Densovirinae
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: unclassified Densovirinae
Supramolecule | Name: unclassified Densovirinae / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 185880 / Sci species name: unclassified Densovirinae / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 210.0 Å / T number (triangulation number): 1 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 36.291906 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP ...String: EGYGKHITSM HVRNIFNQGN QVIRNIVKQQ RYELLDFTGT EAGTTNLPKI IPYQCIWWRG LQNAANVNQT INNMIALNTI SYGVRFLKA KLCIEVYAVT RKRLIQTGAT SYYTDDFEQG QNLFIGWADR KAESIPITTP ADLDETKLTV ANTTLFDANN D NITKEEVP TREKWCHTWD LDVLNHNYLW EPNNLDSQWT LIPGAQAVQP TATPIGPTYQ EIVIATKAIG ANESALVTTI QD RRSYPRL MLSQPQIKDE TDTMKFKYQI RISTELEMEH HIKPDIANPW LTRQTLPLPA LSGDGTTRYV PCVPYETHVS Q UniProtKB: Capsid protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 1.0 x / Component - Name: Phosphate-buffered saline |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: FEI VITROBOT MARK IV |
Details | Recombinantly expressed by the Bac-to-Bac expression system, purified on a sucrose step gradient |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: VOLTA PHASE PLATE |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1700 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.57 µm / Nominal defocus min: 0.5700000000000001 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |