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Yorodumi- PDB-8aay: Nudaurelia capensis omega virus maturation intermediate captured ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aay | ||||||||||||
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Title | Nudaurelia capensis omega virus maturation intermediate captured at pH5.6 (insect cell expressed VLPs): small class from symmetry expansion | ||||||||||||
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: 3.39 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 | 8aay.cif.gz | 412.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aay.ent.gz | 339 KB | Display | PDB format |
PDBx/mmJSON format | 8aay.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aay_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8aay_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8aay_validation.xml.gz | 75.6 KB | Display | |
Data in CIF | 8aay_validation.cif.gz | 114.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aa/8aay ftp://data.pdbj.org/pub/pdb/validation_reports/aa/8aay | HTTPS FTP |
-Related structure data
Related structure data | 15307MC 8a6jC 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: 415 nm / Triangulation number (T number): 4 |
Buffer solution | pH: 5.6 / 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: 2500 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: 49.1 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 16478 Details: Reconstructed from 2 datasets collected at doses of 48.7 and 50.4 electrons per Angstrom squared, respectively. The average of these two values is given. |
-Processing
EM software |
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Image processing | Details: NULL | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353898 Details: Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. ...Details: Particles from an I1 icosahedral consensus map (EMD-15266) were symmetry expanded to C1 and further 3D classified without alignment using a soft mask covering the icosahedral asymmetric unit. The particles for this class were randomly split into half sets for the subsequent reconstruction and postprocessing steps. Note that the symmetry expansion step generates a 60-fold larger particle stack. Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 78 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7ANM Accession code: 7ANM / Source name: PDB / Type: experimental model |