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- EMDB-10103: Cryo-EM structure of murine norovirus (MNV-1) -

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Basic information

Entry
Database: EMDB / ID: EMD-10103
TitleCryo-EM structure of murine norovirus (MNV-1)
Map dataNone
Sample
  • Virus: Murine norovirus 1
    • Protein or peptide: Capsid protein
KeywordsNorovirus / Virus / Capsid / VP1
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / virus-mediated perturbation of host defense response / Capsid protein
Function and homology information
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSnowden JS / Hurdiss DL
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
Wellcome Trust102572/B/13/Z United Kingdom
Medical Research Council (United Kingdom)MR/S007229/1 United Kingdom
CitationJournal: PLoS Biol / Year: 2020
Title: Dynamics in the murine norovirus capsid revealed by high-resolution cryo-EM.
Authors: Joseph S Snowden / Daniel L Hurdiss / Oluwapelumi O Adeyemi / Neil A Ranson / Morgan R Herod / Nicola J Stonehouse /
Abstract: Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically ...Icosahedral viral capsids must undergo conformational rearrangements to coordinate essential processes during the viral life cycle. Capturing such conformational flexibility has been technically challenging yet could be key for developing rational therapeutic agents to combat infections. Noroviruses are nonenveloped, icosahedral viruses of global importance to human health. They are a common cause of acute gastroenteritis, yet no vaccines or specific antiviral agents are available. Here, we use genetics and cryo-electron microscopy (cryo-EM) to study the high-resolution solution structures of murine norovirus as a model for human viruses. By comparing our 3 structures (at 2.9- to 3.1-Å resolution), we show that whilst there is little change to the shell domain of the capsid, the radiating protruding domains are flexible, adopting distinct states both independently and synchronously. In doing so, the capsids sample a range of conformational space, with implications for maintaining virion stability and infectivity.
History
DepositionJul 3, 2019-
Header (metadata) releaseMay 13, 2020-
Map releaseMay 13, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0315
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0315
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s6l
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6s6l
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10103.png

Downloads & links

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Map

FileDownload / File: emd_10103.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 500 pix.
= 532.5 Å		1.07 Å/pix.
x 500 pix.
= 532.5 Å		1.07 Å/pix.
x 500 pix.
= 532.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0315 / Movie #1: 0.0315
Minimum - Maximum-0.26717335 - 0.47851756
Average (Standard dev.)0.0025117847 (±0.020860134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 532.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z532.500532.500532.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-0.2670.4790.003

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Supplemental data

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Mask #1

Fileemd_10103_msk_1.map
Projections & Slices
AxesZYX

Projections

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_10103_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_10103_half_map_2.map
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

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Supramolecule #1: Murine norovirus 1

SupramoleculeName: Murine norovirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RAW264.7 cells / NCBI-ID: 223997 / Sci species name: Murine norovirus 1 / Sci species strain: CW1P3 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus musculus (house mouse)
Virus shellShell ID: 1 / T number (triangulation number): 3

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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: 58.700598 KDa
SequenceString: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL ...String:
MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL WHATQDQEES MRLVCMLYTP LRTNSPGDES FVVSGRLLSK PAADFNFVYL TPPIERTIYR MVDLPVIQPR LC THARWPA PVYGLLVDPS LPSNPQWQNG RVHVDGTLLG TTPISGSWVS CFAAEAAYEF QSGTGEVATF TLIEQDGSAY VPG DRAAPL GYPDFSGQLE IEVQTETTKT GDKLKVTTFE MILGPTTNAD QAPYQGRVFA SVTAAASLDL VDGRVRAVPR SIYG FQDTI PEYNDGLLVP LAPPIGPFLP GEVLLRFRTY MRQIDTADAA AEAIDCALPQ EFVSWFASNA FTVQSEALLL RYRNT LTGQ LLFECKLYNE GYIALSYSGS GPLTFPTDGI FEVVSWVPRL YQLASVGSLA TGRMLKQ

UniProtKB: Capsid protein

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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: 7.6
Component:
ConcentrationFormulaName
200.0 mMNaClSodium chloride
5.0 mMMgCl2Magnesium chloride
1.0 mMKClPotassium chloride
1.0 mMCaCl2Calcium chloride
10.0 mMC8H18N2O4SHEPES
GridMaterial: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 59.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: RELION initial model generation.
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 7811
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6c6q


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-6s6l:
Cryo-EM structure of murine norovirus (MNV-1)

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