|Entry||Database: EMDB / ID: EMD-0294|
|Title||Bacteriophage phi6 dsRNA genome, layer 2|
|Sample||Pseudomonas phage phi6 (bacteriophage):|
|Biological species||Pseudomonas phage phi6 (bacteriophage)|
|Method||single particle reconstruction / cryo EM / Resolution: 13.5 Å|
|Authors||Ilca SL / Huiskonen JT|
|Citation||Journal: Nature / Year: 2019|
Title: Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.
Authors: Serban L Ilca / Xiaoyu Sun / Kamel El Omari / Abhay Kotecha / Felix de Haas / Frank DiMaio / Jonathan M Grimes / David I Stuart / Minna M Poranen / Juha T Huiskonen /
Abstract: Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life ...Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations. Because the release of dsRNA into the cytoplasm triggers host defence mechanisms, dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription. The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10-12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases. However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron microscopy to resolve the dsRNA genome structure of the tri-segmented bacteriophage ɸ6 of the Cystoviridae family, we show that dsRNA viruses can adopt a dsDNA-like single-spooled genome organization. We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. Our results demonstrate that the canonical model for the packing of dsDNA can be extended to dsRNA viruses.
|Structure viewer||EM map: |
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|File||Download / File: emd_0294.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.42 Å|
|Symmetry||Space group: 1|
CCP4 map header:
-Entire Pseudomonas phage phi6
|Entire||Name: Pseudomonas phage phi6 (bacteriophage) / Number of components: 1|
-Component #1: virus, Pseudomonas phage phi6
|Virus||Name: Pseudomonas phage phi6Pseudomonas virus phi6 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SPECIES|
|Species||Species: Pseudomonas phage phi6 (bacteriophage)|
|Specimen||Specimen state: Particle / Method: cryo EM|
|Sample solution||pH: 7.2|
|Vitrification||Cryogen name: ETHANE|
-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: 33 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 55265|
|3D reconstruction||Software: RELION / Resolution: 13.5 Å / Resolution method: FSC 0.143 CUT-OFF|
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