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- EMDB-10127: Thermally-inactivated murine norovirus (MNV-1) -

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Basic information

Entry
Database: EMDB / ID: EMD-10127
TitleThermally-inactivated murine norovirus (MNV-1)
Map dataEM density map for heat-inactivated (hi)MNV, filtered by local resolution.
Sample
  • Virus: Murine norovirus 1
    • Protein or peptide: Murine norovirus (MNV-1) VP1
Biological speciesMurine norovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSnowden JS / Hurdiss DL / Adeyemi OO / Ranson NA / Herod MR / Stonehouse NJ
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MR/S007229/1 United Kingdom
Wellcome Trust102572/B/13/Z 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 16, 2019-
Header (metadata) releaseMay 27, 2020-
Map releaseMay 27, 2020-
UpdateMay 27, 2020-
Current statusMay 27, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0333
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0333
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10127.png

Downloads & links

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Map

FileDownload / File: emd_10127.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density map for heat-inactivated (hi)MNV, filtered by local resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 440 pix.
= 468.6 Å		1.07 Å/pix.
x 440 pix.
= 468.6 Å		1.07 Å/pix.
x 440 pix.
= 468.6 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: 0.0333 / Movie #1: 0.0333
Minimum - Maximum-0.25224268 - 0.4612807
Average (Standard dev.)0.0039663007 (±0.021849113)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 468.60004 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z468.600468.600468.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS440440440
D min/max/mean-0.2520.4610.004

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Supplemental data

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Mask #1

Fileemd_10127_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened density map from 3D refinement.

Fileemd_10127_additional_1.map
AnnotationUnsharpened density map from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened density map.

Fileemd_10127_additional_2.map
AnnotationSharpened density map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map from 3D refinement.

Fileemd_10127_half_map_1.map
AnnotationFirst half map from 3D refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map from 3D refinement.

Fileemd_10127_half_map_2.map
AnnotationSecond half map from 3D refinement.
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 1

EntireName: Murine norovirus 1
Components
  • Virus: Murine norovirus 1
    • Protein or peptide: Murine norovirus (MNV-1) VP1

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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 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 3

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Macromolecule #1: Murine norovirus (MNV-1) VP1

MacromoleculeName: Murine norovirus (MNV-1) VP1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus 1
SequenceString: MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ...String:
MRMSDGAAPK ANGSEASGQD LVPAAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLNP YLAHLSAMYT GWVGNMEVQL VLAGNAFTAG KVVVALVPPY FPKGSLTTAQ ITCFPHVMCD VRTLEPIQLP LLDVRRVLWH ATQDQEESMR LVCMLYTPLR TNSPGDESFV VSGRLLSKPA ADFNFVYLTP PIERTIYRMV DLPVIQPRLC THARWPAPVY GLLVDPSLPS NPQWQNGRVH VDGTLLGTTP ISGSWVSCFA AEAAYEFQSG TGEVATFTLI EQDGSAYVPG DRAAPLGYPD FSGQLEIEVQ TETTKTGDKL KVTTFEMILG PTTNADQAPY QGRVFASVTA AASLDLVDGR VRAVPRSIYG FQDTIPEYND GLLVPLAPPI GPFLPGEVLL RFRTYMRQID TADAAAEAID CALPQEFVSW FASNAFTVQS EALLLRYRNT LTGQLLFECK LYNEGYIALS YSGSGPLTFP TDGIFEVVSW VPRLYQLASV GSLATGRMLK Q

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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: 59.0 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14266
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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