|Entry||Database: EMDB / ID: 3868|
|Title||Cryo-EM single particle reconstruction of Melbournevirus particle.|
|Map data||Melbournevirus capsid(applied inner mask)|
|Method||single particle reconstruction / cryo EM / 26.3 Å resolution|
|Authors||Okamoto K / Miyazaki N / Reddy KNH / Hantke FM / Maia RNCF / Larsson SDD / Abergel C / Claverie JM / Hajdu J / Murata K / Svenda M|
|Citation||Journal: 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.
|Date||Deposition: Sep 12, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Mar 14, 2018 / Last update: Mar 14, 2018|
|Structure viewer||EM map: |
Downloads & links
|File||emd_3868.map.gz (map file in CCP4 format, 2370 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 3.31 Å|
CCP4 map header:
-Entire Melbournevirus particle
|Entire||Name: Melbournevirus particle / Number of components: 1|
-Component #1: virus, Melbournevirus
|Virus||Name: Melbournevirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Source (natural)||Host Species: Acanthamoeba (eukaryote)|
|Shell #1||Name of element: Capsid / Diameter: 2320.0 Å / T number(triangulation number): 309|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||pH: 7.4|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2200FS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Cs: 4.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 5000.0 nm|
|Specimen Holder||Model: JEOL|
|Camera||Detector: TVIPS TEMCAM-F415 (4k x 4k)|
|Processing||Method: single particle reconstruction / Number of projections: 7005|
|3D reconstruction||Software: EMAN2 / Resolution: 26.3 Å / Resolution method: FSC 0.5 CUT-OFF|
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