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- EMDB-0130: Structure of the Macrobrachium rosenbergii Nodavirus -

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Basic information

Entry
Database: EMDB / ID: EMD-0130
TitleStructure of the Macrobrachium rosenbergii Nodavirus
Map dataCryoEM reconstruction of Macrobrachium rosenbergii nodavirus virion
Sample
  • Virus: Macrobrachium rosen (others)
Biological speciesMacrobrachium rosen (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsHo KH / Gabrielsen M
CitationJournal: PLoS Biol / Year: 2018
Title: Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?
Authors: Kok Lian Ho / Mads Gabrielsen / Poay Ling Beh / Chare Li Kueh / Qiu Xian Thong / James Streetley / Wen Siang Tan / David Bhella /
Abstract: Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many ...Macrobrachium rosenbergii nodavirus (MrNV) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations. A detailed understanding of the MrNV virion structure will inform the development of strategies to control outbreaks. The MrNV capsid has also been engineered to display heterologous antigens, and thus knowledge of its atomic resolution structure will benefit efforts to develop tools based on this platform. Here, we present an atomic-resolution model of the MrNV capsid protein (CP), calculated by cryogenic electron microscopy (cryoEM) of MrNV virus-like particles (VLPs) produced in insect cells, and three-dimensional (3D) image reconstruction at 3.3 Å resolution. CryoEM of MrNV virions purified from infected freshwater prawn post-larvae yielded a 6.6 Å resolution structure, confirming the biological relevance of the VLP structure. Our data revealed that unlike other known nodavirus structures, which have been shown to assemble capsids having trimeric spikes, MrNV assembles a T = 3 capsid with dimeric spikes. We also found a number of surprising similarities between the MrNV capsid structure and that of the Tombusviridae: 1) an extensive network of N-terminal arms (NTAs) lines the capsid interior, forming long-range interactions to lace together asymmetric units; 2) the capsid shell is stabilised by 3 pairs of Ca2+ ions in each asymmetric unit; 3) the protruding spike domain exhibits a very similar fold to that seen in the spikes of the tombusviruses. These structural similarities raise questions concerning the taxonomic classification of MrNV.
History
DepositionJul 13, 2018-
Header (metadata) releaseAug 22, 2018-
Map releaseNov 7, 2018-
UpdateNov 7, 2018-
Current statusNov 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0130.png

Downloads & links

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Map

FileDownload / File: emd_0130.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM reconstruction of Macrobrachium rosenbergii nodavirus virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 512 pix.
= 568.32 Å		1.11 Å/pix.
x 512 pix.
= 568.32 Å		1.11 Å/pix.
x 512 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.016487258 - 0.09236631
Average (Standard dev.)0.003213234 (±0.010186772)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z568.320568.320568.320
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0160.0920.003

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Supplemental data

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Sample components

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Entire : Macrobrachium rosen

EntireName: Macrobrachium rosen (others)
Components
  • Virus: Macrobrachium rosen (others)

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Supramolecule #1: Macrobrachium rosen

SupramoleculeName: Macrobrachium rosen / type: virus / ID: 1 / Parent: 0
Details: Virions were purified from Macrobrachium rosenbergii infected post-larvae
NCBI-ID: 32644 / Sci species name: Macrobrachium rosen / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macrobrachium rosenbergii (giant freshwater prawn)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: 25mM HEPES, 150 mM NaCl; pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Virions were loaded onto Quantifoil R2/2 grids which had a continuous carbon film added. Virions were adsorbed to the carbon for 1 minute prior to blotting (4s)..
DetailsPurified virions

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Electron microscopy

MicroscopeJEOL 2200FS
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-40 / Number real images: 263 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER

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Image processing

DetailsMovies were processed to correct for movement and electron dose using Motioncor2
Particle selectionNumber selected: 7236 / Details: Autopicking in Relion
CTF correctionSoftware - Name: RELION (ver. 2.1) / Details: Defocus estimation by GCTF
Startup modelType of model: OTHER / Details: Gaussian Sphere
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 3931
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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