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- EMDB-71603: Cryo-EM structure of VX93 Fab in complex with GII.4 Norovirus P domain -

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Basic information

Entry
Database: EMDB / ID: EMD-71603
TitleCryo-EM structure of VX93 Fab in complex with GII.4 Norovirus P domain
Map datastructure of VX93 Fab in complex with GII.4 Norovirus P domain
Sample
  • Complex: VX93 Fab in complex with GII.4 Norovirus P domain
    • Protein or peptide: VP1
    • Protein or peptide: VX93 heavy chain
    • Protein or peptide: VX93 light chain
KeywordsNorovirus / Antibody complex / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / VP1
Function and homology information
Biological speciesHomo sapiens (human) / Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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
DepositionJul 4, 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_71603.png

Downloads & links

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Map

FileDownload / File: emd_71603.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of VX93 Fab in complex with GII.4 Norovirus P domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 Å		0.73 Å/pix.
x 420 pix.
= 304.5 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: 0.022
Minimum - Maximum-0.08108059 - 0.13746543
Average (Standard dev.)0.000016849162 (±0.0024436135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 304.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_71603_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_71603_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : VX93 Fab in complex with GII.4 Norovirus P domain

EntireName: VX93 Fab in complex with GII.4 Norovirus P domain
Components
  • Complex: VX93 Fab in complex with GII.4 Norovirus P domain
    • Protein or peptide: VP1
    • Protein or peptide: VX93 heavy chain
    • Protein or peptide: VX93 light chain

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Supramolecule #1: VX93 Fab in complex with GII.4 Norovirus P domain

SupramoleculeName: VX93 Fab in complex with GII.4 Norovirus P domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Molecular weightTheoretical: 34.215129 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPSKPFSVPV LTVEEMTNSR FPIPLEKLFT GPSSAFVVQP QNGRCTTDGV LLGTTQLSPV NICTFRGDVT HITGSRNYTM NLASQNWND YDPTEEIPAP LGTPDFVGKI QGVLTQTTRT DGSTRGHKAT VYTGSADFAP KLGRVQFETD TDRDFEANQN T KFTPVGVI ...String:
GPSKPFSVPV LTVEEMTNSR FPIPLEKLFT GPSSAFVVQP QNGRCTTDGV LLGTTQLSPV NICTFRGDVT HITGSRNYTM NLASQNWND YDPTEEIPAP LGTPDFVGKI QGVLTQTTRT DGSTRGHKAT VYTGSADFAP KLGRVQFETD TDRDFEANQN T KFTPVGVI QDGGTTHRNE PQQWVLPSYS GRNTHNVHLA PAVAPTFPGE QLLFFRSTMP GCSGYPNMDL DCLLPQEWVQ YF YQEAAPA QSDVALLRFV NPDTGRVLFE CKLHKSGYVT VAHTGQHDLV IPPNGYFRFD SWVNQFYTLA PM

UniProtKB: VP1

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Macromolecule #2: VX93 heavy chain

MacromoleculeName: VX93 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.104677 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPG LVKPSQTLSL TCTVSGVFIR TGGYYWTWIR HRPGKGLEWI GHVYYNGDSF YNPSLESRVA ISVDTSKNQF SLRLHSVTA ADTAEYFCVR GWFSSSYYRL DYFDSWGQGA QVTVSP

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Macromolecule #3: VX93 light chain

MacromoleculeName: VX93 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.571962 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVLTQSPDS LAVSLGERAT INCKSSQSIF YSSNNKNYLA WYQKKPGQPP KQIFYWASTR ESGVPDRFTG SGSGTDFTLT INSLQAEDV AVYYCQQYYS IPLTFGPGTK VDIK

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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

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
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: 3620 / Average exposure time: 3.03 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: 2.0 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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.0) / Number images used: 332242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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