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

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Basic information

Entry
Database: EMDB / ID: EMD-3868
TitleCryo-EM single particle reconstruction of Melbournevirus particle.
Map dataMelbournevirus capsid(applied inner mask)
SampleMelbournevirus particle != Melbournevirus

Melbournevirus particle

  • Virus: Melbournevirus
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 26.3 Å
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.
History
DepositionSep 12, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseMar 14, 2018-
UpdateMar 14, 2018-
Current statusMar 14, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3868.png

Downloads & links

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Map

FileDownload / File: emd_3868.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMelbournevirus capsid(applied inner mask)
Voxel sizeX=Y=Z: 3.31 Å
Density
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.99535125 - 1.470726
Average (Standard dev.)-0.016885828 (±0.2911426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions840840840
Spacing840840840
CellA=B=C: 2780.4 Å
α=β=γ: 90.0 °

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
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 particle

EntireName: Melbournevirus particle
Components
  • Virus: Melbournevirus

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Supramolecule #1: Melbournevirus

SupramoleculeName: Melbournevirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1560514 / Sci species name: Melbournevirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba (eukaryote)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 2320.0 Å / T number (triangulation number): 309

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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: 7.4
GridModel: R1.2/1.3 Quantifoil Micro Tools GmbH / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 7005
CTF correctionSoftware - Name: EMAN2
Startup modelType of model: INSILICO MODEL
In silico model: Random initial model was generated by EMAN2 software.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 26.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 7005
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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