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- EMDB-9739: Cryo-EM structure of Human Norovirus GII.3 VLP with the resting P... -

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Basic information

Entry
Database: EMDB / ID: EMD-9739
TitleCryo-EM structure of Human Norovirus GII.3 VLP with the resting P-domain conformation
Map dataHuman Norovirus GII.3 VLP with the resting P-domain conformation
Sample
  • Virus: Human Norovirus GII.3 TCH04-577
Biological speciesHuman Norovirus GII.3 TCH04-577
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsSong C / Todaka R / Miki M / Haga K / Fujimoto A / Yokoyama M / Miyazaki N / Iwasaki K / Murakami 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: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9739.png

Downloads & links

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Map

FileDownload / File: emd_9739.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman Norovirus GII.3 VLP with the resting P-domain conformation
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 400 pix.
= 568.8 Å		1.42 Å/pix.
x 400 pix.
= 568.8 Å		1.42 Å/pix.
x 400 pix.
= 568.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.422 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.14349198 - 0.32401446
Average (Standard dev.)0.009073667 (±0.030492865)
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-0.1430.3240.009

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Supplemental data

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Sample components

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Entire : Human Norovirus GII.3 TCH04-577

EntireName: Human Norovirus GII.3 TCH04-577
Components
  • Virus: Human Norovirus GII.3 TCH04-577

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Supramolecule #1: Human Norovirus GII.3 TCH04-577

SupramoleculeName: Human Norovirus GII.3 TCH04-577 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 106516 / Sci species name: Human Norovirus GII.3 TCH04-577 / Sci species strain: U201 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Baculovirus / 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
TemperatureMin: 76.0 K / Max: 77.0 K
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
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: 106 / Average exposure time: 3.0 sec. / Average electron dose: 15.0 e/Å2
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 FIELD / Cs: 4.2 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 40000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 279
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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