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

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Basic information

Entry
Database: EMDB / ID: 0130
TitleStructure of the Macrobrachium rosenbergii Nodavirus
Map dataCryoEM reconstruction of Macrobrachium rosenbergii nodavirus virion
SampleMacrobrachium rosen:
virus
SourceMacrobrachium rosen (others)
Methodsingle particle reconstruction / cryo EM / 6.6 Å resolution
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
DateDeposition: Jul 13, 2018 / Header (metadata) release: Aug 22, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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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

Downloads & links

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Map

Fileemd_0130.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.11 Å/pix.
= 568.32 Å
512 pix
1.11 Å/pix.
= 568.32 Å
512 pix
1.11 Å/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
Contour Level:0.035 (by author), 0.035 (movie #1):
Minimum - Maximum-0.016487258 - 0.09236631
Average (Standard dev.)0.003213234 (0.010186772)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 568.32 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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
Details: Virions were purified from Macrobrachium rosenbergii infected post-larvae
Number of components: 1

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Component #1: virus, Macrobrachium rosen

VirusName: Macrobrachium rosen / Class: VIRION
Details: Virions were purified from Macrobrachium rosenbergii infected post-larvae
Empty: No / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Macrobrachium rosen (others)
Source (natural)Host Species: Macrobrachium rosenbergii
Shell #1Name of element: Capsid / Diameter: 400.0 Å / T number(triangulation number): 3

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.2 mg/ml / Buffer solution: 25mM HEPES, 150 mM NaCl; pH 7.4 / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
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)..

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Energy filter: In-column Omega Filter
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image acquisition

Image acquisitionNumber of digital images: 263

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 3931
Details: Movies were processed to correct for movement and electron dose using Motioncor2
3D reconstructionSoftware: RELION / CTF correction: Defocus estimation by GCTF / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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