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- EMDB-3655: Cryo-Electron Microscopy Structure of the Macrobrachium rosenberg... -

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Basic information

Entry
Database: EMDB / ID: EMD-3655
TitleCryo-Electron Microscopy Structure of the Macrobrachium rosenbergii Nodavirus Capsid at 7 Angstroms Resolution
Map dataMacrobrachium rosenbergii nodavirus virus-like particle.
SampleMacrobrachium rosenbergii Nodavirus Capsid != Macrobrachium rosenbergii Nodavirus

Macrobrachium rosenbergii Nodavirus Capsid

  • Virus: Macrobrachium rosenbergii Nodavirus
Biological speciesMacrobrachium rosenbergii Nodavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsBhella D / Ho KL
CitationJournal: Sci Rep / Year: 2017
Title: Cryo-Electron Microscopy Structure of the Macrobrachium rosenbergii Nodavirus Capsid at 7 Angstroms Resolution.
Authors: Kok Lian Ho / Chare Li Kueh / Poay Ling Beh / Wen Siang Tan / David Bhella /
Abstract: White tail disease in the giant freshwater prawn Macrobrachium rosenbergii causes significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing ...White tail disease in the giant freshwater prawn Macrobrachium rosenbergii causes significant economic losses in shrimp farms and hatcheries and poses a threat to food-security in many developing countries. Outbreaks of Macrobrachium rosenbergii nodavirus (MrNV), the causative agent of white tail disease (WTD) are associated with up to 100% mortality rates. There are no interventions available to treat or prevent MrNV disease however. Here we show the structure of MrNV virus-like particles (VLPs) produced by recombinant expression of the capsid protein, using cryogenic electron microscopy. Our data show that MrNV VLPs package nucleic acids in a manner reminiscent of other known nodavirus structures. The structure of the capsid however shows striking differences from insect and fish infecting nodaviruses, which have been shown to assemble trimer-clustered T = 3 icosahedral virus particles. MrNV particles have pronounced dimeric blade-shaped spikes extending up to 6 nm from the outer surface of the capsid shell. Our structural analysis supports the assertion that MrNV may belong to a new genus of the Nodaviridae. Moreover, our study provides the first structural view of an important pathogen affecting aquaculture industries across the world.
History
DepositionMar 29, 2017-
Header (metadata) releaseApr 5, 2017-
Map releaseMay 31, 2017-
UpdateJul 12, 2017-
Current statusJul 12, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3655.png

Downloads & links

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Map

FileDownload / File: emd_3655.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMacrobrachium rosenbergii nodavirus virus-like particle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 512 pix.
= 558.08 Å		1.09 Å/pix.
x 512 pix.
= 558.08 Å		1.09 Å/pix.
x 512 pix.
= 558.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.14659674 - 0.20144895
Average (Standard dev.)0.0033128622 (±0.014665142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 558.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z558.080558.080558.080
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1470.2010.003

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Supplemental data

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Sample components

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Entire : Macrobrachium rosenbergii Nodavirus Capsid

EntireName: Macrobrachium rosenbergii Nodavirus Capsid
Components
  • Virus: Macrobrachium rosenbergii Nodavirus

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Supramolecule #1: Macrobrachium rosenbergii Nodavirus

SupramoleculeName: Macrobrachium rosenbergii Nodavirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 222557 / Sci species name: Macrobrachium rosenbergii Nodavirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macrobrachium rosenbergii (giant freshwater prawn)
Virus shellShell ID: 1 / 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

BufferpH: 7.2
GridModel: Protochips C-flat R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
Details: C-flats had an additional carbon evaporation applied
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot for 4 seconds, Blot force 25.

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Electron microscopy

MicroscopeJEOL 2200FSC
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Frames/image: 2-60 / Number grids imaged: 4 / Number real images: 281 / Average exposure time: 3.0 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 9592
CTF correctionSoftware - Name: RELION (ver. 2.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4ftb


Details: Flock House virus PDB file was rendered to a 3D density map using pdb2mrc (EMAN).
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 1658
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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