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Yorodumi- PDB-8a6j: Nudaurelia capensis omega virus maturation intermediate captured ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a6j | ||||||||||||
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Title | Nudaurelia capensis omega virus maturation intermediate captured at pH6.25 (insect cell expressed VLPs) | ||||||||||||
Components | p70 | ||||||||||||
Keywords | VIRUS LIKE PARTICLE / ICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / VIRUS-LIKE PARTICLE | ||||||||||||
Function / homology | Peptidase N2 / Peptidase family A21 / Viral coat protein subunit / p70 Function and homology information | ||||||||||||
Biological species | Nudaurelia capensis omega virus | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||
Authors | Castells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: To be published Title: Decoding virus maturation with cryo-EM structures of intermediates Authors: Castells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a6j.cif.gz | 380 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a6j.ent.gz | 318.7 KB | Display | PDB format |
PDBx/mmJSON format | 8a6j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a6j_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 8a6j_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 8a6j_validation.xml.gz | 72.1 KB | Display | |
Data in CIF | 8a6j_validation.cif.gz | 108.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a6/8a6j ftp://data.pdbj.org/pub/pdb/validation_reports/a6/8a6j | HTTPS FTP |
-Related structure data
Related structure data | 15209MC 8aayC 8ac6C 8achC 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: 69891.953 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nudaurelia capensis omega virus / Cell (production host): sf21 cell line / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q4TVS9 |
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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: Nudaurelia capensis omega virus / Type: VIRUS / Details: expressed in Spodoptera frugiperda Sf21 cells / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 16.76 MDa / Experimental value: NO |
Source (natural) | Organism: Nudaurelia capensis omega virus |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21 |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Gonimbrasia cytherea |
Virus shell | Name: coat / Diameter: 460 nm / Triangulation number (T number): 4 |
Buffer solution | pH: 6.25 / Details: NULL |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: NULL |
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1 sec. / Electron dose: 50.4 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10528 / Details: NULL |
-Processing
EM software |
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Image processing | Details: NULL | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114943 / Details: NULL / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 432 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8A3C |