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Yorodumi- PDB-8eu6: Acheta domesticus segmented densovirus high buoyancy fraction 1 (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eu6 | ||||||
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Title | Acheta domesticus segmented densovirus high buoyancy fraction 1 (HB1) empty capsid structure | ||||||
Components | Capsid protein | ||||||
Keywords | VIRUS LIKE PARTICLE / parvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / virus | ||||||
Function / homology | Capsid protein Function and homology information | ||||||
Biological species | Solenopsis invicta-associated densovirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | ||||||
Authors | Penzes, J.J. / McKenna, R. / Tijssen, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2023 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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eu6.cif.gz | 119.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eu6.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 8eu6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eu6_validation.pdf.gz | 854.2 KB | Display | wwPDB validaton report |
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Full document | 8eu6_full_validation.pdf.gz | 859.3 KB | Display | |
Data in XML | 8eu6_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8eu6_validation.cif.gz | 25.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/8eu6 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/8eu6 | HTTPS FTP |
-Related structure data
Related structure data | 28605MC 8er8C 8erkC 8eu7C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 36291.906 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Solenopsis invicta-associated densovirus Gene: CP / Production host: Acheta domesticus (house cricket) / References: UniProt: A0A891H5C3 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: unclassified Densovirinae / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: unclassified Densovirinae (virus) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Acheta domesticus |
Buffer solution | pH: 7.4 |
Buffer component | Conc.: 1 x / Name: Phosphate buffered saline |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Deceased common house crickets, previously showing signs of paralysis, inability to jump, and inability to control movement |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: OTHER / Nominal defocus max: 4000 nm / Nominal defocus min: 810 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 970 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
-Processing
Software | Name: PHENIX / Version: 1.10-2155_2155: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 46082 | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30065 / Num. of class averages: 5 / Symmetry type: POINT | ||||||||||||||||||||||||
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