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- EMDB-27847: Mouse norovirus strain CR6, attenuated -

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Basic information

Entry
Database: EMDB / ID: EMD-27847
TitleMouse norovirus strain CR6, attenuated
Map dataMouse norovirus strain C6
Sample
  • Virus: Murine norovirus GV/CR6/2005/USA
KeywordsVirus / norovirus / attenuated / bile
Biological speciesMurine norovirus GV/CR6/2005/USA
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSmith TJ / Sherman M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01-AI141465 United States
CitationJournal: Front Immunol / Year: 2022
Title: Environmentally-triggered contraction of the norovirus virion determines diarrheagenic potential.
Authors: Emily W Helm / Amy M Peiper / Matthew Phillips / Caroline G Williams / Michael B Sherman / Theresa Kelley / Hong Q Smith / Sorin O Jacobs / Dhairya Shah / Sarah M Tatum / Neha Iyer / Marco ...Authors: Emily W Helm / Amy M Peiper / Matthew Phillips / Caroline G Williams / Michael B Sherman / Theresa Kelley / Hong Q Smith / Sorin O Jacobs / Dhairya Shah / Sarah M Tatum / Neha Iyer / Marco Grodzki / Joyce C Morales Aparicio / Elizabeth A Kennedy / Mikayla S Manzi / Megan T Baldridge / Thomas J Smith / Stephanie M Karst /
Abstract: Noroviruses are the leading cause of severe childhood diarrhea and foodborne disease worldwide. While they are a major cause of disease in all age groups, infections in the very young can be quite ...Noroviruses are the leading cause of severe childhood diarrhea and foodborne disease worldwide. While they are a major cause of disease in all age groups, infections in the very young can be quite severe with annual estimates of 50,000-200,000 fatalities in children under 5 years old. In spite of the remarkable disease burden associated with norovirus infections in people, very little is known about the pathogenic mechanisms underlying norovirus diarrhea, principally because of the lack of tractable small animal models. We recently demonstrated that wild-type neonatal mice are susceptible to murine norovirus (MNV)-induced acute self-resolving diarrhea in a time course mirroring human norovirus disease. Using this robust pathogenesis model system, we demonstrate that virulence is regulated by the responsiveness of the viral capsid to environmental cues that trigger contraction of the VP1 protruding (P) domain onto the particle shell, thus enhancing receptor binding and infectivity. The capacity of a given MNV strain to undergo this contraction positively correlates with infection of cells expressing low abundance of the virus receptor CD300lf, supporting a model whereby virion contraction triggers infection of CD300lf cell types that are responsible for diarrhea induction. These findings directly link environmentally-influenced biophysical features with norovirus disease severity.
History
DepositionAug 16, 2022-
Header (metadata) releaseJul 26, 2023-
Map releaseJul 26, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27847.png

Downloads & links

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Map

FileDownload / File: emd_27847.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMouse norovirus strain C6
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 520 pix.
= 572. Å		1.1 Å/pix.
x 520 pix.
= 572. Å		1.1 Å/pix.
x 520 pix.
= 572. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-3.9236546 - 5.960416
Average (Standard dev.)0.008202949 (±0.2622004)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 572.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mouse norovirus strain C6

Fileemd_27847_half_map_1.map
AnnotationMouse norovirus strain C6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mouse norovirus strain C6

Fileemd_27847_half_map_2.map
AnnotationMouse norovirus strain C6
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Murine norovirus GV/CR6/2005/USA

EntireName: Murine norovirus GV/CR6/2005/USA
Components
  • Virus: Murine norovirus GV/CR6/2005/USA

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Supramolecule #1: Murine norovirus GV/CR6/2005/USA

SupramoleculeName: Murine norovirus GV/CR6/2005/USA / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 463722 / Sci species name: Murine norovirus GV/CR6/2005/USA / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104309
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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