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- EMDB-9740: Cryo-EM structure of Human Norovirus GII.3 VLP with the rising P-... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9740 | |||||||||||||||
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Title | Cryo-EM structure of Human Norovirus GII.3 VLP with the rising P-domain conformation | |||||||||||||||
![]() | Human Norovirus GII.3 VLP with the rising P-domain conformation | |||||||||||||||
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Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | |||||||||||||||
![]() | Song C / Todaka R / Miki M / Haga K / Fujimoto A / Yokoyama M / Miyazaki N / Iwasaki K / Murakami K / Katayama K / Murata K | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 52.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.6 KB 15.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 196.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9735C ![]() 9736C ![]() 9737C ![]() 9738C ![]() 9739C ![]() 9741C ![]() 6iukC C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Human Norovirus GII.3 VLP with the rising P-domain conformation | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.422 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Human Norovirus GII.3 TCH04-577
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Human Norovirus GII.3 TCH04-577
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Host system | Organism: ![]() |
Virus shell | Shell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: amorphous ice |
Grid | Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K |
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Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 76.0 K / Max: 77.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV |
Image recording | Film 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: 1917 / Average exposure time: 3.0 sec. / Average electron dose: 15.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER Cooling holder cryogen: NITROGEN |