|Entry||Database: EMDB / ID: 6713|
|Title||Inner capsid of Rice Dwarf Virus with T-trimers|
|Sample||Rice dwarf virus (isolate O):|
|Source||Rice dwarf virus (isolate O)|
|Method||single particle reconstruction / cryo EM / 13.43 Å resolution|
|Authors||Nakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Murata K / Nakagawa A|
|Citation||Journal: Structure / Year: 2018|
Title: An Assembly Intermediate Structure of Rice Dwarf Virus Reveals a Hierarchical Outer Capsid Shell Assembly Mechanism.
Authors: Yusuke Nakamichi / Naoyuki Miyazaki / Kenta Tsutsumi / Akifumi Higashiura / Hirotaka Narita / Kazuyoshi Murata / Atsushi Nakagawa
Abstract: Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric ...Nearly all viruses of the Reoviridae family possess a multi-layered capsid consisting of an inner layer with icosahedral T = 1 symmetry and a second-outer layer (composed of 260 copies of a trimeric protein) exhibiting icosahedral T = 13 symmetry. Here we describe the construction and structural evaluation of an assembly intermediate of the Rice dwarf virus of the family Reoviridae stalled at the second capsid layer via targeted disruption of the trimer-trimer interaction interface in the second-layer capsid protein. Structural determination was performed by conventional and Zernike/Volta phase-contrast cryoelectron microscopy. The assembly defect second-layer capsid trimers bound exclusively to the outer surface of the innermost capsid layer at the icosahedral 3-fold axis. Furthermore, the second-layer assembly could not proceed without specific inter-trimer interactions. Our results suggest that the correct assembly pathway for second-layer capsid formation is highly controlled at the inter-layer and inter-trimer interactions.
|Date||Deposition: Mar 14, 2017 / Header (metadata) release: Jun 27, 2018 / Map release: Jun 27, 2018 / Last update: Jan 16, 2019|
|Structure viewer||EM map: |
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|File||emd_6713.map.gz (map file in CCP4 format, 256001 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.88 Å|
CCP4 map header:
-Entire Rice dwarf virus (isolate O)
|Entire||Name: Rice dwarf virus (isolate O) / Number of components: 1|
-Component #1: virus, Rice dwarf virus (isolate O)
|Virus||Name: Rice dwarf virus (isolate O) / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Species||Species: Rice dwarf virus (isolate O)|
|Source (natural)||Host Species: Rice|
|Shell #1||Name of element: inner shell / T number(triangulation number): 1|
|Shell #2||Name of element: outer shell / T number(triangulation number): 13|
|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||Imaging mode: BRIGHT FIELD / Energy filter: omega / Energy window: 0-20 eV|
|Specimen Holder||Model: GATAN LIQUID NITROGEN|
|Camera||Detector: TVIPS TEMCAM-F415 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 784|
|3D reconstruction||Software: RELION / Resolution: 13.43 Å / Resolution method: FSC 0.143 CUT-OFF|
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