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Yorodumi- PDB-8er8: Acheta domesticus segmented densovirus, mature virion capsid structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 8er8 | ||||||||||||
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Title | Acheta domesticus segmented densovirus, mature virion capsid structure | ||||||||||||
Components |
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Keywords | VIRUS/DNA / parvovirus / densovirus / virus capsid / virion / insect virus / capsid / invertebrate / VIRUS-DNA complex | ||||||||||||
Function / homology | DNA / DNA (> 10) / DNA (> 100) Function and homology information | ||||||||||||
Biological species | unclassified Densovirinae (virus) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | ||||||||||||
Authors | Penzes, J.J. / McKenna, R. / Tijssen, P. | ||||||||||||
Funding support | United States, 3items
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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 | 8er8.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8er8.ent.gz | 101.6 KB | Display | PDB format |
PDBx/mmJSON format | 8er8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8er8_validation.pdf.gz | 924.4 KB | Display | wwPDB validaton report |
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Full document | 8er8_full_validation.pdf.gz | 933.9 KB | Display | |
Data in XML | 8er8_validation.xml.gz | 19.8 KB | Display | |
Data in CIF | 8er8_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/8er8 ftp://data.pdbj.org/pub/pdb/validation_reports/er/8er8 | HTTPS FTP |
-Related structure data
Related structure data | 28550MC 8erkC 8eu6C 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
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 37793.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Densovirinae (virus) |
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#2: DNA chain | Mass: 39820.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Densovirinae (virus) |
-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: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Acheta domesticus |
Virus shell | Name: Acheta domesticus segmented densovirus capsid / Diameter: 210 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7.4 |
Buffer component | Conc.: 1 x / Name: Phosphate-buffered saline |
Specimen | Conc.: 2 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: 90 % |
-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: 650 nm / Cs: 2.7 mm |
Image recording | Electron dose: 75 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1411 |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 188074 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150469 / Algorithm: FOURIER SPACE / Num. of class averages: 5 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3UX1 Pdb chain-ID: A / Accession code: 3UX1 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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