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- EMDB-10755: Cryo-EM structure of norovirus GII.4c VLP with T=4 icosahedral sy... -

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Basic information

Entry
Database: EMDB / ID: EMD-10755
TitleCryo-EM structure of norovirus GII.4c VLP with T=4 icosahedral symmetry
Map dataCryo-EM structure of GII.4c VLPs expressed in H5 insect cells with T=4 icosahedral symmetry
Sample
  • Virus: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a
Biological speciesNorovirus 06-AM-11/2006/GII.4/Yerseke/2006a
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
AuthorsDevant JM / Hansman GS
CitationJournal: Virology / Year: 2021
Title: Structural heterogeneity of a human norovirus vaccine candidate.
Authors: Jessica M Devant / Grant S Hansman /
Abstract: Human norovirus virus-like particles (VLPs) are assumed to be morphologically and antigenically similar to virion particles. The norovirus virion is assembled from 180 copies of the capsid protein ...Human norovirus virus-like particles (VLPs) are assumed to be morphologically and antigenically similar to virion particles. The norovirus virion is assembled from 180 copies of the capsid protein (VP1) and exhibits T = 3 icosahedral symmetry. In this study, we showed that the vaccine candidate GII.4c VP1 formed T = 1 and T = 3 VLPs, but mainly assembled into T = 4 icosahedral particles that were composed of 240 VP1 copies. In contrast, another clinically important genotype, GII.17, almost exclusively folded into T = 3 VLPs. Interestingly, the GII.4c T = 1 particles had higher binding capacities to norovirus-specific Nanobodies than to GII.4c T = 3 and T = 4 particles. Our data indicated that the occluded Nanobody-binding epitopes on the T = 1 particles were more accessible compared to the larger T = 3 and T = 4 particles. Overall, this new data revealed that GII.4c VLPs had a preference for forming the T = 4 icosahedral symmetry and future studies with varied sized norovirus VLPs should take caution when examining antigenicity.
History
DepositionMar 12, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateApr 14, 2021-
Current statusApr 14, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.227
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.227
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10755.png

Downloads & links

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Map

FileDownload / File: emd_10755.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of GII.4c VLPs expressed in H5 insect cells with T=4 icosahedral symmetry
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 500 pix.
= 687.5 Å		1.38 Å/pix.
x 500 pix.
= 687.5 Å		1.38 Å/pix.
x 500 pix.
= 687.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.227 / Movie #1: 0.227
Minimum - Maximum-1.0452597 - 1.8187201
Average (Standard dev.)0.0026077982 (±0.099995226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 687.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3751.3751.375
M x/y/z500500500
origin x/y/z0.0000.0000.000
length x/y/z687.500687.500687.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS500500500
D min/max/mean-1.0451.8190.003

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Supplemental data

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Sample components

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Entire : Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a

EntireName: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a
Components
  • Virus: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a

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Supramolecule #1: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a

SupramoleculeName: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1631306
Sci species name: Norovirus 06-AM-11/2006/GII.4/Yerseke/2006a
Sci species strain: GII.4c / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: Trichoplusia ni (cabbage looper) / Recombinant strain: HighFive insect cells
Virus shellShell ID: 1 / Diameter: 520.0 Å / T number (triangulation number): 4

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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

Concentration2 mg/mL
BufferpH: 7.4 / Component - Name: PBS / Details: PBS buffer
GridModel: Quantifoil R0.6/1 / Material: COPPER/RHODIUM / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 3983 / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.4.0) / Number images used: 118971
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.4.0)

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