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- PDB-8a3c: Nudaurelia capensis omega virus maturation intermediate captured ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8a3c
TitleNudaurelia capensis omega virus maturation intermediate captured at pH5.9 (insect cell expressed VLPs)
Componentsp70
KeywordsVIRUS LIKE PARTICLE / ICOSAHEDRAL VIRUS / AUTO-CATALYTIC CLEAVAGE / VIRUS MATURATION / VIRUS-LIKE PARTICLE
Function / homologyPeptidase N2 / Peptidase family A21 / virion component / Viral coat protein subunit / p70
Function and homology information
Biological speciesNudaurelia capensis omega virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsCastells-Graells, R. / Hesketh, E.L. / Johnson, J.E. / Ranson, N.A. / Lawson, D.M. / Lomonossoff, G.P.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L014130/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/J/000PR9794 United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: To be published
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
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p70
B: p70
C: p70
D: p70


Theoretical massNumber of molelcules
Total (without water)279,5684
Polymers279,5684
Non-polymers00
Water00
1
A: p70
B: p70
C: p70
D: p70
x 60


Theoretical massNumber of molelcules
Total (without water)16,774,069240
Polymers16,774,069240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein
p70


Mass: 69891.953 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nudaurelia capensis omega virus / Production host: Spodoptera frugiperda (fall armyworm) / Tissue (production host): Sf21 cell line / References: UniProt: Q4TVS9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nudaurelia capensis omega virus / Type: VIRUS / Details: expressed in Spodoptera frugiperda Sf21 cells / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 16.76 MDa / Experimental value: NO
Source (natural)Organism: Nudaurelia capensis omega virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Gonimbrasia cytherea
Virus shellName: coat / Diameter: 460 nm / Triangulation number (T number): 4
Buffer solutionpH: 5.9 / Details: NULL
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: NULL
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN
Image recordingAverage 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
IDNameVersionCategory
1RELION3.0.3particle selection
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.14model fitting
8Coot0.9model fitting
10RELION3.0.3initial Euler assignment
11RELION3.0.3final Euler assignment
12RELION3.0.3classification
13RELION3.0.33D reconstruction
14PHENIX1.20rc4model refinement
Image processingDetails: NULL
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 38792 / Details: NULL / Symmetry type: POINT
Atomic model buildingB value: 233 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 7ANM

7anm


Accession code: 7ANM / Source name: PDB / Type: experimental model

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