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- EMDB-4899: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in Nic... -

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Basic information

Entry
Database: EMDB / ID: EMD-4899
TitleAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana
Map dataAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (local resolution filtered map).
Sample
  • Virus: Betanodavirus sp.
    • Protein or peptide: Coat protein
KeywordsBetanodavirus / Virus-like particle / Virus / Vaccine / VIRUS LIKE PARTICLE
Function / homologyNodavirus capsid / nodavirus capsid protein / T=3 icosahedral viral capsid / Viral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesBetanodavirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHurdiss DL / Ranson NA
Funding support United Kingdom, 4 items
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, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rj0
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rj0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4899.png

Downloads & links

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Map

FileDownload / File: emd_4899.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (local resolution filtered map).
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0138 / Movie #1: 0.0138
Minimum - Maximum-0.04114394 - 0.07030399
Average (Standard dev.)0.00027246008 (±0.004644915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0410.0700.000

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Supplemental data

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Additional map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_additional.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (unsharpened map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_half_map_1.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (half map one).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_half_map_2.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (half map two).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Betanodavirus sp.

EntireName: Betanodavirus sp.
Components
  • Virus: Betanodavirus sp.
    • Protein or peptide: Coat protein

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Supramolecule #1: Betanodavirus sp.

SupramoleculeName: Betanodavirus sp. / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1906674 / Sci species name: Betanodavirus sp. / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Gadus morhua (Atlantic cod)
Molecular weightTheoretical: 7.7 MDa
Virus shellShell ID: 1 / T number (triangulation number): 3

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Betanodavirus sp.
Molecular weightTheoretical: 36.903711 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: VRKGNKKLAK QATTKAVNPQ PRRRNNNRRR GMRADAPLAK ASTITGFGRG TNDVHLTGMS RIAQAVIPAG TGTDGYIVVD ETIVPELLP RLGFAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDSDHTFDA IQATRGAVVA KWWESRTIRP Q YARALLWT ...String:
VRKGNKKLAK QATTKAVNPQ PRRRNNNRRR GMRADAPLAK ASTITGFGRG TNDVHLTGMS RIAQAVIPAG TGTDGYIVVD ETIVPELLP RLGFAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDSDHTFDA IQATRGAVVA KWWESRTIRP Q YARALLWT SVGKEQRLTS PGRLILLCVG NNTDVVNVSV LCRWSVRLSV PSLETPEDTF APILTLGPLY NDSLAANDFK SI LLGSTQL DIAPEGAVYS LDRPLSIDYN LGTGDVDRAV YWHVKKVAGN AGTPAGWFHW GLWDNFNKTF TQGTAYYSDA QPR QILLPV GTLFTRADSG N

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.2
Details: PBS (140 mM NaCl, 15 mM KH2PO4, 80 mM Na2HPO4, 27 mM KCl, pH 7.2)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 2359 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20887
Startup modelType of model: OTHER / Details: Low resolution cryo-EM map generated in-house.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 16616
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4wiz


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 137 / Target criteria: Cross-correlation coefficient
Output model

PDB-6rj0:
Atlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana

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