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- EMDB-9736: Cryo-EM structure of Murine Norovirus S7 virion with the rising P... -

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Basic information

Entry
Database: EMDB / ID: EMD-9736
TitleCryo-EM structure of Murine Norovirus S7 virion with the rising P-domain conformation
Map dataMurine norovirus S7 virion with the rising P-domain conformation
Sample
  • Virus: Murine norovirus S7
Biological speciesMurine norovirus S7
Methodsingle particle reconstruction / cryo EM / Resolution: 7.2 Å
AuthorsSong C / Todaka R / Miki M / Haga K / Fujimoto A / Yokoyama M / Miyazaki N / Iwasaki K / Muratami K / Katayama K / Murata K
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fk0108034h0602 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP26102545 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101072j0001 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-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_9736.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMurine norovirus S7 virion with the rising P-domain conformation
Voxel sizeX=Y=Z: 1.422 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.08535848 - 0.17841707
Average (Standard dev.)0.0047958563 (±0.01640103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 568.80005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4221.4221.422
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z568.800568.800568.800
α/β/γ90.00090.00090.000
start NX/NY/NZ434333
NX/NY/NZ116118137
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0850.1780.005

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Supplemental data

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Sample components

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Entire : Murine norovirus S7

EntireName: Murine norovirus S7
Components
  • Virus: Murine norovirus S7

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Supramolecule #1: Murine norovirus S7

SupramoleculeName: Murine norovirus S7 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 357231 / Sci species name: Murine norovirus S7 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Mus musculus (house mouse)
Host systemOrganism: baculovirus / Recombinant cell: RAW264.7 / Recombinant plasmid: cDNA
Virus shellShell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3

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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
GridModel: Quantifoil R1.2/1.3 / Material: MOLYBDENUM
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 40.0 µm / Calibrated defocus max: 4.9672 µm / Calibrated defocus min: 1.5783 µm / Calibrated magnification: 45065 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 4.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 76.0 K / Max: 77.0 K
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 3-75 / Number real images: 2739 / Average exposure time: 3.0 sec. / Average electron dose: 15.0 e/Å2

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final 3D classificationSoftware - Name: RELION (ver. 2.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 5063
FSC plot (resolution estimation)

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