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- EMDB-72542: Cryo-EM map of norovirus GII.4 SY 2012 VLP in complex with VX93 F... -

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Basic information

Entry
Database: EMDB / ID: EMD-72542
TitleCryo-EM map of norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold axis local map (4 Fabs)
Map data
Sample
  • Complex: Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold axis local map (4 Fabs)
KeywordsNorovirus / Antibody complex / VIRAL PROTEIN / VIRUS LIKE PARTICLE
Biological speciesNorovirus GII.4 Sydney 2012
Methodsingle particle reconstruction / cryo EM / Resolution: 6.97 Å
AuthorsJo G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Serum IgA proteomics reveals clonal composition and neutralization of dimeric and monomeric IgA repertoires against human norovirus.
Authors: Juyeon Park / Gyunghee Jo / Yaoska Reyes / Whitney Pickens / Dae Sung Kim / Alexandra Beaver / Verónica P Costantini / Chang Liu / Daeun Kim / Daechan Park / Victoria Longo / Paul D Brewer- ...Authors: Juyeon Park / Gyunghee Jo / Yaoska Reyes / Whitney Pickens / Dae Sung Kim / Alexandra Beaver / Verónica P Costantini / Chang Liu / Daeun Kim / Daechan Park / Victoria Longo / Paul D Brewer-Jensen / Michael L Mallory / Ed Satterwhite / Rocio Zapata-Bustos / Jeffrey Marchioni / Mark R Zweigart / Becca A Flitter / Jan Vinjé / Julianna Han / Ted M Ross / Jiwon Lee / Jason J Lavinder / Sean N Tucker / Zunlong Ke / Andrew B Ward / Lisa C Lindesmith / Ralph S Baric / George Georgiou /
Abstract: Protection against human norovirus correlates with attachment ligand blockade antibody titers, fecal IgA titers, and serum IgA titers. IgA responses in serum comprise approximately 80 to 95% of ...Protection against human norovirus correlates with attachment ligand blockade antibody titers, fecal IgA titers, and serum IgA titers. IgA responses in serum comprise approximately 80 to 95% of monomeric IgA (mIgA) and 5 to 20% of dimeric IgA (dIgA). Using serum LC-MS/MS proteomics, we established clonal relationships between circulating IgG and IgA, as well as between dIgA and mIgA. We observed a modest degree of clonal overlap between circulating IgG and IgA at steady state and found that more than 80% of antigen-specific mIgA was also detectable as dIgA. We biochemically characterized neutralizing epitopes on norovirus GII.4 virus-like particles (VLPs) targeted by serum IgA clonotypes and demonstrated that dIgA markedly enhances neutralization potency relative to mIgA and IgG in an epitope-specific manner. Cryoelectron microscopy and cryoelectron tomography revealed that whether IgA dimerization enhances viral neutralization depends on epitope accessibility on the VLP and antibody binding orientation. Together, these findings provide molecular-level resolution of the serum IgA response and define the structural basis by which dIgA enhances neutralization potency in an epitope-specific manner.
History
DepositionSep 8, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72542.png

Downloads & links

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Map

FileDownload / File: emd_72542.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 348. Å		0.73 Å/pix.
x 480 pix.
= 348. Å		0.73 Å/pix.
x 480 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.069160216 - 0.13684322
Average (Standard dev.)0.00039992415 (±0.0046100947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_72542_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_72542_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold a...

EntireName: Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold axis local map (4 Fabs)
Components
  • Complex: Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold axis local map (4 Fabs)

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Supramolecule #1: Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold a...

SupramoleculeName: Norovirus GII.4 SY 2012 VLP in complex with VX93 Fab - fivefold axis local map (4 Fabs)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Norovirus GII.4 Sydney 2012

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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

Concentration0.8 mg/mL
BufferpH: 6 / Details: PBS
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 3750 / Average exposure time: 3.47 sec. / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC - ab initio
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 175518
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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