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- PDB-8a3c: Nudaurelia capensis omega virus maturation intermediate captured ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8a3c | ||||||||||||
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Title | Nudaurelia capensis omega virus maturation intermediate captured at pH5.9 (insect cell expressed VLPs) | ||||||||||||
![]() | p70 | ||||||||||||
![]() | 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![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||||||||
![]() | Castells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Nudaurelia capensis omega virus maturation intermediate captured at pH5.9 (insect cell expressed VLPs) 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 375.4 KB | Display | ![]() |
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PDB format | ![]() | 314.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 81 KB | Display | |
Data in CIF | ![]() | 119.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15112MC ![]() 8a41C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() ![]() |
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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 |
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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: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
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: 5.9 / 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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 1 sec. / Electron dose: 46 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10010 / Details: NULL |
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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: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38792 / Details: NULL / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 233 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7ANM |