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- EMDB-3868: Cryo-EM single particle reconstruction of Melbournevirus particle. -

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Basic information

Entry
Database: EMDB / ID: 3868
TitleCryo-EM single particle reconstruction of Melbournevirus particle.
Map dataMelbournevirus capsid(applied inner mask)
SampleMelbournevirus
SourceMelbournevirus / virus
Methodsingle particle reconstruction, at 26.3 Å resolution
AuthorsOkamoto K / Miyazaki N / Reddy KNH / Hantke FM / Maia RNCF / Larsson SDD / Abergel C / Claverie JM / Hajdu J / Murata K / Svenda M
CitationJournal: Virology / Year: 2018
Title: Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly.
Authors: Kenta Okamoto / Naoyuki Miyazaki / Hemanth K N Reddy / Max F Hantke / Filipe R N C Maia / Daniel S D Larsson / Chantal Abergel / Jean-Michel Claverie / Janos Hajdu / Kazuyoshi Murata / Martin Svenda
Abstract: Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron ...Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.
Copyright: 2018 Elsevier Inc. All rights reserved.
DateDeposition: Sep 12, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Mar 14, 2018 / Last update: Mar 14, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_3868.map.gz (map file in CCP4 format, 2370 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
840 pix
3.31 Å/pix.
= 2780.4 Å
840 pix
3.31 Å/pix.
= 2780.4 Å
840 pix
3.31 Å/pix.
= 2780.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.31 Å
Density
Contour Level:0.6 (by author), 0.6 (movie #1):
Minimum - Maximum-0.99535125 - 1.470726
Average (Standard dev.)-0.016885828 (0.2911426)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions840840840
Origin000
Limit839839839
Spacing840840840
CellA=B=C: 2780.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z840840840
origin x/y/z0.0000.0000.000
length x/y/z2780.4002780.4002780.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS840840840
D min/max/mean-0.9951.471-0.017

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Supplemental data

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Sample components

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Entire Melbournevirus

EntireName: Melbournevirus / Number of components: 1

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Component #1: virus, Melbournevirus

VirusName: Melbournevirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Melbournevirus / virus
Source (natural)Host Species: Acanthamoeba / eukaryote /
Shell #1Name of element: Capsid / Diameter: 2320.0 Å / T number(triangulation number): 309

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 4.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 5000.0 nm
Specimen HolderModel: JEOL
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7005
3D reconstructionSoftware: EMAN2 / Resolution: 26.3 Å / Resolution method: FSC 0.5 CUT-OFF

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