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- EMDB-27322: Murine norovirus strain WU23 at pH 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-27322
TitleMurine norovirus strain WU23 at pH 5
Map dataMurine norovirus strain WU23 at pH 5
Sample
  • Virus: Norovirus
Biological speciesNorovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSmith TJ
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
DepositionJun 15, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27322.png

Downloads & links

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Map

FileDownload / File: emd_27322.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMurine norovirus strain WU23 at pH 5
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 540 pix.
= 594. Å		1.1 Å/pix.
x 540 pix.
= 594. Å		1.1 Å/pix.
x 540 pix.
= 594. 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: 0.55
Minimum - Maximum-5.063032 - 6.890753
Average (Standard dev.)0.0040394077 (±0.28515804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 594.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Murine norovirus strain WU23 at pH 5

Fileemd_27322_half_map_1.map
AnnotationMurine norovirus strain WU23 at pH 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Murine norovirus strain WU23 at pH 5

Fileemd_27322_half_map_2.map
AnnotationMurine norovirus strain WU23 at pH 5
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Norovirus

EntireName: Norovirus
Components
  • Virus: Norovirus

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Supramolecule #1: Norovirus

SupramoleculeName: Norovirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 142786 / Sci species name: Norovirus / Virus type: VIRION / Virus isolate: SEROTYPE / 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 / Details: PBS no metals pH 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 325309
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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