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- EMDB-8917: Single-particle reconstruction of reovirus T1L/T3D M2 -

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Basic information

Entry
Database: EMDB / ID: EMD-8917
TitleSingle-particle reconstruction of reovirus T1L/T3D M2
Map dataSurface rendering of Reovirus T1L/T3D M2
SampleReovirus != Reovirus sp.

Reovirus

  • Virus: Reovirus sp.
Biological speciesReovirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsSnyder AJ / Wang JCY / Danthi P
CitationJournal: J Virol / Year: 2019
Title: Components of the Reovirus Capsid Differentially Contribute to Stability.
Authors: Anthony J Snyder / Joseph Che-Yen Wang / Pranav Danthi /
Abstract: The mammalian orthoreovirus (reovirus) outer capsid is composed of 200 μ1-σ3 heterohexamers and a maximum of 12 σ1 trimers. During cell entry, σ3 is degraded by luminal or intracellular proteases ...The mammalian orthoreovirus (reovirus) outer capsid is composed of 200 μ1-σ3 heterohexamers and a maximum of 12 σ1 trimers. During cell entry, σ3 is degraded by luminal or intracellular proteases to generate the infectious subviral particle (ISVP). When ISVP formation is prevented, reovirus fails to establish a productive infection, suggesting proteolytic priming is required for entry. ISVPs are then converted to ISVP*s, which is accompanied by μ1 rearrangements. The μ1 and σ3 proteins confer resistance to inactivating agents; however, neither the impact on capsid properties nor the mechanism (or basis) of inactivation is fully understood. Here, we utilized T1L/T3D M2 and T3D/T1L S4 to investigate the determinants of reovirus stability. Both reassortants encode mismatched subunits. When μ1-σ3 were derived from different strains, virions resembled wild-type particles in structure and protease sensitivity. T1L/T3D M2 and T3D/T1L S4 ISVPs were less thermostable than wild-type ISVPs. In contrast, virions were equally susceptible to heating. Virion associated μ1 adopted an ISVP*-like conformation concurrent with inactivation; σ3 preserves infectivity by preventing μ1 rearrangements. Moreover, thermostability was enhanced by a hyperstable variant of μ1. Unlike the outer capsid, the inner capsid (core) was highly resistant to elevated temperatures. The dual layered architecture allowed for differential sensitivity to inactivating agents. Nonenveloped and enveloped viruses are exposed to the environment during transmission to a new host. Protein-protein and/or protein-lipid interactions stabilize the particle and protect the viral genome. Mammalian orthoreovirus (reovirus) is composed of two concentric, protein shells. The μ1 and σ3 proteins form the outer capsid; contacts between neighboring subunits are thought to confer resistance to inactivating agents. We further investigated the determinants of reovirus stability. The outer capsid was disrupted concurrent with the loss of infectivity; virion associated μ1 rearranged into an altered conformation. Heat sensitivity was controlled by σ3; however, particle integrity was enhanced by a single μ1 mutation. In contrast, the inner capsid (core) displayed superior resistance to heating. These findings reveal structural components that differentially contribute to reovirus stability.
History
DepositionJun 25, 2018-
Header (metadata) releaseJul 4, 2018-
Map releaseJul 4, 2018-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8917.png

Downloads & links

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Map

FileDownload / File: emd_8917.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSurface rendering of Reovirus T1L/T3D M2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 400 pix.
= 1000. Å		2.5 Å/pix.
x 400 pix.
= 1000. Å		2.5 Å/pix.
x 400 pix.
= 1000. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005 / Movie #1: 0.005
Minimum - Maximum-0.017227948 - 0.019669883
Average (Standard dev.)0.00026220706 (±0.003331825)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 1000.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z1000.0001000.0001000.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0170.0200.000

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Supplemental data

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Sample components

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Entire : Reovirus

EntireName: Reovirus
Components
  • Virus: Reovirus sp.

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Supramolecule #1: Reovirus sp.

SupramoleculeName: Reovirus sp. / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10891 / Sci species name: Reovirus sp. / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Mus musculus (house mouse)

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL 3200FS
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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