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Yorodumi- PDB-8t9x: Zophobas morio black wasting virus strain NJ2-molitor virion structure -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t9x | |||||||||
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Title | Zophobas morio black wasting virus strain NJ2-molitor virion structure | |||||||||
Components |
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Keywords | VIRUS/DNA / Capsid / Virion / Parvovirus / Densovirus / Invertebrate / Insect / Pathogen / ssDNA / VIRUS / VIRUS-DNA complex | |||||||||
Function / homology | DNA Function and homology information | |||||||||
Biological species | Zophobas morio black wasting virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å | |||||||||
Authors | Penzes, J.J. / Kaelber, J.T. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Sequencing-free discovery by cryo-EM of a pathogenic parvovirus causing mass mortality of farmed beetles Authors: Penzes, J.J. / Holm, M. / Firlar, E. / Kaelber, J.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t9x.cif.gz | 170 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t9x.ent.gz | 133.3 KB | Display | PDB format |
PDBx/mmJSON format | 8t9x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8t9x_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8t9x_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8t9x_validation.xml.gz | 39.7 KB | Display | |
Data in CIF | 8t9x_validation.cif.gz | 53.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t9/8t9x ftp://data.pdbj.org/pub/pdb/validation_reports/t9/8t9x | HTTPS FTP |
-Related structure data
Related structure data | 41125MC 8t9cC 8t9eC 8ta7C 8tjeC 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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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 48085.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus |
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#2: DNA chain | Mass: 886.637 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus |
#3: DNA chain | Mass: 2733.827 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus |
#4: DNA chain | Mass: 1504.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Zophobas morio black wasting virus |
#5: Water | ChemComp-HOH / |
-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: Zophobas morio densovirus / Type: VIRUS Details: Purified from T. molitor larvae, which were asymptomatic Entity ID: #1-#4 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Zophobas morio densovirus / Strain: NJ2-molitor |
Details of virus | Empty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Tenebrio molitor |
Virus shell | Diameter: 28 nm / Triangulation number (T number): 1 |
Buffer solution | pH: 7.4 |
Buffer component | Conc.: 1 x / Name: Phosphate-buffered saline / Formula: PBS |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Purified virus from homogenized T. molitor larval tissue |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293 K |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 156329 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15964 / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||
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