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- EMDB-0295: Bacteriophage phi6 dsRNA genome, layer 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-0295
TitleBacteriophage phi6 dsRNA genome, layer 3
Map databacteriophage phi6 dsRNA genome, layer 3
Sample
  • Virus: Pseudomonas phage phi6 (bacteriophage)
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 16.2 Å
AuthorsIlca SL / Huiskonen JT
CitationJournal: 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.
History
DepositionOct 18, 2018-
Header (metadata) releaseJan 16, 2019-
Map releaseJun 12, 2019-
UpdateAug 28, 2019-
Current statusAug 28, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.008
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0295.png

Downloads & links

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Map

FileDownload / File: emd_0295.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacteriophage phi6 dsRNA genome, layer 3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 512 pix.
= 727.04 Å		1.42 Å/pix.
x 512 pix.
= 727.04 Å		1.42 Å/pix.
x 512 pix.
= 727.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008 / Movie #1: 0.008
Minimum - Maximum-0.017267335 - 0.028841568
Average (Standard dev.)0.00013630345 (±0.00104567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-254-254-254
Dimensions512512512
Spacing512512512
CellA=B=C: 727.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.421.421.42
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z727.040727.040727.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-254-254-254
NC/NR/NS512512512
D min/max/mean-0.0170.0290.000

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Supplemental data

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Sample components

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Entire : Pseudomonas phage phi6

EntireName: Pseudomonas phage phi6 (bacteriophage)
Components
  • Virus: Pseudomonas phage phi6 (bacteriophage)

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Supramolecule #1: Pseudomonas phage phi6

SupramoleculeName: Pseudomonas phage phi6 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10879 / Sci species name: Pseudomonas phage phi6 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 16.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0.3)
Software - details: Custom version to relax symmetry multi-modal priors
Number images used: 55265
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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