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Yorodumi- PDB-8eu5: Acheta domesticus segmented densovirus high buoyancy fraction 2 e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eu5 | ||||||||||||
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Title | Acheta domesticus segmented densovirus high buoyancy fraction 2 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: 3.1 Å | ||||||||||||
Authors | Penzes, J.J. / McKenna, R. / Tijssen, P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Structural and molecular biology of Acheta domesticus segmented densovirus, the first parvovirus to harbor a bipartite genome Authors: Penzes, J.J. / Pham, H.T. / Chipman, P. / Smith, E. / McKenna, R. / Tijssen, P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eu5.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eu5.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 8eu5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eu5_validation.pdf.gz | 777 KB | Display | wwPDB validaton report |
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Full document | 8eu5_full_validation.pdf.gz | 783.5 KB | Display | |
Data in XML | 8eu5_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 8eu5_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eu/8eu5 ftp://data.pdbj.org/pub/pdb/validation_reports/eu/8eu5 | HTTPS FTP |
-Related structure data
Related structure data | 28604MC 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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1 |
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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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Source (natural) | Organism: unclassified Densovirinae (virus) |
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Virus shell | Diameter: 210 nm / Triangulation number (T number): 1 |
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: 4320 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Phase plate: VOLTA PHASE PLATE |
-Processing
Software | Name: PHENIX / Version: 1.10_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: 58680 | ||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48354 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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