Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.
Journal, issue, pages	Nature, Vol. 570, Issue 7760, Page 252-256, Year 2019
Publish date	May 29, 2019
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 /
PubMed 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.
External links	Nature / PubMed:31142835
Methods	EM (single particle)
Resolution	3.5 - 16.9 Å
Structure data	EMDB-0294: Bacteriophage phi6 dsRNA genome, layer 2 Method: EM (single particle) / Resolution: 13.5 Å EMDB-0295: Bacteriophage phi6 dsRNA genome, layer 3 Method: EM (single particle) / Resolution: 16.2 Å EMDB-0296: Bacteriophage phi6 dsRNA genome, layers 4 and 5 Method: EM (single particle) / Resolution: 16.9 Å 0299 6hy0 EMDB-0299: Bacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry PDB-6hy0: Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry Method: EM (single particle) / Resolution: 3.5 Å EMDB-0300: Reconstruction of dsRNA bacteriophage phi6 nucleocapsid with D3 symmetry Method: EM (single particle) / Resolution: 4.0 Å EMDB-0302: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo D3' Method: EM (single particle) / Resolution: 8.0 Å EMDB-0304: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo D3', sub-conformation 1 Method: EM (single particle) / Resolution: 9.7 Å EMDB-0305: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo D3', sub-conformation 2 Method: EM (single particle) / Resolution: 10.2 Å EMDB-0306: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo D3', sub-conformation 3 Method: EM (single particle) / Resolution: 10.2 Å EMDB-10075: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo D3 Method: EM (single particle) / Resolution: 7.2 Å EMDB-10289: Bacteriophage phi6 dsRNA genome, layer 1, conformation pseudo C2 Method: EM (single particle) / Resolution: 8.0 Å
Source	pseudomonas phage phi6 (bacteriophage)
Keywords	VIRUS / dsRNA / capsid