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- EMDB-8916: Single-particle reconstruction of reovirus T1L -

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Basic information

Entry
Database: EMDB / ID: 8916
TitleSingle-particle reconstruction of reovirus T1L
Map dataSurface rendering of Reovirus T1L
SampleReovirusReoviridae:
virus
SourceReovirus sp.
Methodsingle particle reconstruction / cryo EM / 8.2 Å resolution
AuthorsSnyder AJ / Wang JCY / Danthi P
CitationJournal: J. Virol. / Year: 2018
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. In this report, 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 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.
DateDeposition: Jun 25, 2018 / Header (metadata) release: Jul 4, 2018 / Map release: Jul 4, 2018 / Last update: Nov 14, 2018

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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

Downloads & links

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Map

Fileemd_8916.map.gz (map file in CCP4 format, 256001 KB)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
2.5 Å/pix.
= 1000. Å
400 pix
2.5 Å/pix.
= 1000. Å
400 pix
2.5 Å/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
Contour Level:0.005 (by author), 0.005 (movie #1):
Minimum - Maximum-0.019065678 - 0.021191198
Average (Standard dev.)0.0002982313 (0.0031632492)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin0.00.00.0
Limit399.0399.0399.0
Spacing400400400
CellA=B=C: 1000.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0190.0210.000

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Supplemental data

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Sample components

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Entire Reovirus

EntireName: Reovirus / Number of components: 1

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Component #1: virus, Reovirus sp.

VirusName: Reovirus sp. / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Reovirus sp.
Source (engineered)Expression System: Mus musculus (house mouse)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 10568
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF

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