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- EMDB-9741: Cryo-EM structure of Murine Norovirus S7 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-9741
TitleCryo-EM structure of Murine Norovirus S7 VLP
Map dataCryo-EM map of MNV-S7 VLP
Sample
  • Virus: Murine norovirus GV
    • Protein or peptide: Major capsid protein VP1
KeywordsVLP / mature / stable / VIRUS
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 / Capsid protein
Function and homology information
Biological speciesMurine norovirus GV/NIH-2410/2005/USA / Murine norovirus GV
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSong C / Miyazaki N / Iwasaki K / Katayama K / Murata K / Yokoyama M / Murakami K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0108034h0602 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072j0001 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP26102545 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP16H00786 Japan
CitationJournal: PLoS Pathog / Year: 2020
Title: Dynamic rotation of the protruding domain enhances the infectivity of norovirus.
Authors: Chihong Song / Reiko Takai-Todaka / Motohiro Miki / Kei Haga / Akira Fujimoto / Ryoka Ishiyama / Kazuki Oikawa / Masaru Yokoyama / Naoyuki Miyazaki / Kenji Iwasaki / Kosuke Murakami / ...Authors: Chihong Song / Reiko Takai-Todaka / Motohiro Miki / Kei Haga / Akira Fujimoto / Ryoka Ishiyama / Kazuki Oikawa / Masaru Yokoyama / Naoyuki Miyazaki / Kenji Iwasaki / Kosuke Murakami / Kazuhiko Katayama / Kazuyoshi Murata /
Abstract: Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines ...Norovirus is the major cause of epidemic nonbacterial gastroenteritis worldwide. Lack of structural information on infection and replication mechanisms hampers the development of effective vaccines and remedies. Here, using cryo-electron microscopy, we show that the capsid structure of murine noroviruses changes in response to aqueous conditions. By twisting the flexible hinge connecting two domains, the protruding (P) domain reversibly rises off the shell (S) domain in solutions of higher pH, but rests on the S domain in solutions of lower pH. Metal ions help to stabilize the resting conformation in this process. Furthermore, in the resting conformation, the cellular receptor CD300lf is readily accessible, and thus infection efficiency is significantly enhanced. Two similar P domain conformations were also found simultaneously in the human norovirus GII.3 capsid, although the mechanism of the conformational change is not yet clear. These results provide new insights into the mechanisms of non-enveloped norovirus transmission that invades host cells, replicates, and sometimes escapes the hosts immune system, through dramatic environmental changes in the gastrointestinal tract.
History
DepositionNov 28, 2018-
Header (metadata) releaseFeb 26, 2020-
Map releaseFeb 26, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

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

emd_9741.png

Downloads & links

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Map

FileDownload / File: emd_9741.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of MNV-S7 VLP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 600 pix.
= 516. Å		0.86 Å/pix.
x 600 pix.
= 516. Å		0.86 Å/pix.
x 600 pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.08431751 - 0.15500742
Average (Standard dev.)0.0012706635 (±0.007721407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 516.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000516.000
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0840.1550.001

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Supplemental data

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Sample components

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Entire : Murine norovirus GV

EntireName: Murine norovirus GV
Components
  • Virus: Murine norovirus GV
    • Protein or peptide: Major capsid protein VP1

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Supramolecule #1: Murine norovirus GV

SupramoleculeName: Murine norovirus GV / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 463708 / Sci species name: Murine norovirus GV / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Mus musculus (house mouse)
Virus shellShell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3

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Macromolecule #1: Major capsid protein VP1

MacromoleculeName: Major capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine norovirus GV/NIH-2410/2005/USA
Molecular weightTheoretical: 58.833785 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MRMSDGAAPK ANGSEASGQD LVPTAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL ...String:
MRMSDGAAPK ANGSEASGQD LVPTAVEQAV PIQPVAGAAL AAPAAGQINQ IDPWIFQNFV QCPLGEFSIS PRNTPGEILF DLALGPGLN PYLAHLSAMY TGWVGNMEVQ LVLAGNAFTA GKVVVALVPP YFPKGSLTTA QITCFPHVMC DVRTLEPIQL P LLDVRRVL WHATQDQEES MRLVCMLYTP LRTNSPGDES FVVSGRLLSK PAADFNFVYL TPPIERTIYR MVDLPVLQPR LC THARWPA PIYGLLVDPS LPSNPQWQNG RVHVDGTLLG TTPVSGSWVS CFAAEAAYEF QSGIGEVATF TLIEQDGSAY VPG DRAAPL GYPDFSGQLE IEVQTETTKK GEKLKVTTFE MILGPTTNVD QVPYQGRVYA SLTAAASLDL VDGRVRAVPR SVYG FQDVV PEYNDGLLVP LAPPIGPFLP GEVLLRFRTY MRQIDSTDAA AEAIDCALPQ EFVSWFASNA FTVQSEALLL RYRNT LTGQ LLFECKLYSE GYIALSYSGS GPLTFPTDGF FEVVSWVPRL YQLASVGSLA TGRTLKQ

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: 7.4
Sugar embeddingMaterial: amorphous ice
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 76.0 K / Max: 77.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 3-31 / Number real images: 2746 / Average exposure time: 2.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 41847
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 157
Output model

PDB-6iuk:
Cryo-EM structure of Murine Norovirus capsid

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