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- EMDB-42600: Murine norovirus in the presence of 1mM calcium -

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Basic information

Entry
Database: EMDB / ID: EMD-42600
TitleMurine norovirus in the presence of 1mM calcium
Map dataMurine norovirus in the presence of calcium
Sample
  • Virus: Murine norovirus 1
    • Protein or peptide: Capsid protein
  • Ligand: CALCIUM ION
  • Ligand: water
Keywordsmurine / norovirus / metals / activation / VIRAL PROTEIN
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / virion component / Viral coat protein subunit / : / Capsid protein
Function and homology information
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsSmith TJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141465 United States
CitationJournal: J Virol / Year: 2024
Title: The reversible activation of norovirus by metal ions.
Authors: Michael Sherman / Faith Cox / Hong Smith / Mohamed H Habib / Stephanie Karst / Christiane E Wobus / Thomas J Smith /
Abstract: Murine norovirus (MNV) undergoes extremely large conformational changes in response to the environment. The = 3 icosahedral capsid is composed of 180 copies of ~58-kDa VP1 comprised of N-terminus (N) ...Murine norovirus (MNV) undergoes extremely large conformational changes in response to the environment. The = 3 icosahedral capsid is composed of 180 copies of ~58-kDa VP1 comprised of N-terminus (N), shell (S), and C-terminal protruding (P) domains. At neutral pH, the P domains are loosely tethered to the shell and float ~15 Å above the surface. At low pH or in the presence of bile salts, the P domain drops onto the shell and this movement is accompanied by conformational changes within the P domain that enhance receptor interactions while blocking antibody binding. While previous crystallographic studies identified metal binding sites in the isolated P domain, the ~2.7-Å cryo-electron microscopy structures of MNV in the presence of Mg or Ca presented here show that metal ions can recapitulate the contraction observed at low pH or in the presence of bile. Further, we show that these conformational changes are reversed by dialysis against EDTA. As observed in the P domain crystal structures, metal ions bind to and contract the G'H' loop. This movement is correlated with the lifting of the C'D' loop and rotation of the P domain dimers about each other, exposing the bile salt binding pocket. Isothermal titration calorimetry experiments presented here demonstrate that the activation signals (bile salts, low pH, and metal ions) act in a synergistic manner that, individually, all result in the same activated structure. We present a model whereby these reversible conformational changes represent a uniquely dynamic and tissue-specific structural adaptation to the environment.IMPORTANCEThe highly mobile protruding domains on the calicivirus capsids are recognized by cell receptor(s) and antibodies. At neutral pH, they float ~15 Å above the shell but at low pH or in the presence of bile salts, they contract onto the surface. Concomitantly, changes within the P domain block antibody binding while enhancing receptor binding. While we previously demonstrated that metals also block antibody binding, it was unknown whether they might also cause similar conformational changes in the virion. Here, we present the near atomic cryo-electron microscopy structures of infectious murine norovirus (MNV) in the presence of calcium or magnesium ions. The metal ions reversibly induce the same P domain contraction as low pH and bile salts and act in a synergistic manner with the other stimuli. We propose that, unlike most other viruses, MNV facilely changes conformations as a unique means to escape immune surveillance as it moves through various tissues.
History
DepositionNov 2, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42600.png

Downloads & links

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Map

FileDownload / File: emd_42600.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMurine norovirus in the presence of calcium
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: 1.15
Minimum - Maximum-8.079018 - 11.093514000000001
Average (Standard dev.)0.0029637315 (±0.4745209)
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: MNV calcium half map A

Fileemd_42600_half_map_1.map
AnnotationMNV calcium half map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: MNV calcium half map B

Fileemd_42600_half_map_2.map
AnnotationMNV calcium half map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Murine norovirus 1

EntireName: Murine norovirus 1
Components
  • Virus: Murine norovirus 1
    • Protein or peptide: Capsid protein
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Murine norovirus 1

SupramoleculeName: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
Molecular weightTheoretical: 56.136617 KDa
SequenceString: SGQDLVPAAV EQAVPIQPVA GAALAAPAAG QINQIDPWIF QNFVQCPLGE FSISPRNTPG EILFDLALGP GLNPYLAHLS AMYTGWVGN MEVQLVLAGN AFTAGKVVVA LVPPYFPKGS LTTAQITCFP HVMCDVRTLE PIQLPLLDVR RVLWHATQDQ E ESMRLVCM ...String:
SGQDLVPAAV EQAVPIQPVA GAALAAPAAG QINQIDPWIF QNFVQCPLGE FSISPRNTPG EILFDLALGP GLNPYLAHLS AMYTGWVGN MEVQLVLAGN AFTAGKVVVA LVPPYFPKGS LTTAQITCFP HVMCDVRTLE PIQLPLLDVR RVLWHATQDQ E ESMRLVCM LYTPLRTNSP GDESFVVSGR LLSKPAADFN FVYLTPPIER TIYRMVDLPV IQPRLCTHAR WPAPVYGLLV DP SLPSNPQ WQNGRVHVDG TLLGTTPISG SWVSCFAAEA AYEFQSGTGE VATFTLIEQD GSAYVPGDRA APLGYPDFSG QLE IEIQTE TTKTGDKLKV TTFEMILGPT TNADQAPYQG RVFASVTAAA SLDLVDGRVR AVPRSIYGFQ DTIPEYNDGL LVPL APPIG PFLPGEVLLR FRTYMRQIDT ADAAAEAIDC ALPQEFVSWF ASNAFTVQSE ALLLRYRNTL TGQLLFECKL YNEGY IALS YSGSGPLTFP TDGIFEVVSW VPRLYQLASV GS

UniProtKB: Capsid protein

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 310 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77727
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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