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- PDB-6rj0: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in Nic... -

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Basic information

Entry
Database: PDB / ID: 6rj0
TitleAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / Betanodavirus / Virus-like particle / Virus / Vaccine
Function / homologyNodavirus capsid / nodavirus capsid protein / T=3 icosahedral viral capsid / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta / Capsid protein alpha
Function and homology information
Biological speciesBetanodavirus sp.
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHurdiss, D.L. / Ranson, N.A.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M027856/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/J/000PR9794 United Kingdom
Wellcome Trust102572/B/13/Z United Kingdom
CitationJournal: Front Plant Sci / Year: 2019
Title: Plant-Made Nervous Necrosis Virus-Like Particles Protect Fish Against Disease.
Authors: Johanna Marsian / Daniel L Hurdiss / Neil A Ranson / Anneli Ritala / Richard Paley / Irene Cano / George P Lomonossoff /
Abstract: Virus-like particles (VLPs) of the fish virus, Atlantic Cod Nervous necrosis virus (ACNNV), were successfully produced by transient expression of the coat protein in plants. VLPs could also be ...Virus-like particles (VLPs) of the fish virus, Atlantic Cod Nervous necrosis virus (ACNNV), were successfully produced by transient expression of the coat protein in plants. VLPs could also be produced in transgenic tobacco BY-2 cells. The protein extracted from plants self-assembled into = 3 particles, that appeared to be morphologically similar to previously analyzed NNV VLPs when analyzed by high resolution cryo-electron microscopy. Administration of the plant-produced VLPs to sea bass () showed that they could protect the fish against subsequent virus challenge, indicating that plant-produced vaccines may have a substantial future role in aquaculture.
History
DepositionApr 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.3Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]

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Structure visualization

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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein


Theoretical massNumber of molelcules
Total (without water)110,7113
Polymers110,7113
Non-polymers00
Water0
1
A: Coat protein
B: Coat protein
C: Coat protein
x 60


Theoretical massNumber of molelcules
Total (without water)6,642,668180
Polymers6,642,668180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
MethodUCSF CHIMERA

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Components

#1: Protein Coat protein


Mass: 36903.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betanodavirus sp. / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q91D83*PLUS

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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: Betanodavirus sp. / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 7.7 MDa / Experimental value: NO
Source (natural)Organism: Betanodavirus sp.
Source (recombinant)Organism: Nicotiana benthamiana (plant)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Gadus morhua
Virus shellTriangulation number (T number): 3
Buffer solutionpH: 7.2
Details: PBS (140 mM NaCl, 15 mM KH2PO4, 80 mM Na2HPO4, 27 mM KCl, pH 7.2)
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 281 K

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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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 2359
Image scansMovie frames/image: 20

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatchparticle selection
2EPUimage acquisition
4GctfCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
13RELION23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 20887
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16616 / Symmetry type: POINT
Atomic model buildingB value: 137 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model buildingPDB-ID: 4WIZ

4wiz

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