|Entry||Database: EMDB / ID: EMD-6989|
|Title||Inner capsid of Rice Dwarf Virus with T-trimers (Full particle)|
|Sample||Rice dwarf virus:|
|Biological species||Rice dwarf virus|
|Method||single particle reconstruction / cryo EM / Resolution: 6.4 Å|
|Authors||Nakamichi Y / Miyazaki N / Tsutsumi K / Higashiura A / Narita H / Murata K / Nakagawa A|
|Citation||Journal: Structure / Year: 2019|
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.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_6989.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.39 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Rice dwarf virus
|Entire||Name: Rice dwarf virus / Number of components: 1|
-Component #1: virus, Rice dwarf virus
|Virus||Name: Rice dwarf virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: SPECIES|
|Species||Species: Rice dwarf virus|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 6|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 47000.0 X (nominal) / Cs: 0.1 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -1200.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (90.0 - 95.0 K)|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 2804 / Sampling size: 14 µm|
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