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- PDB-9pfk: Cryo-EM structure of VX93 Fab in complex with GII.4 Norovirus P domain -

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Basic information

Entry
Database: PDB / ID: 9pfk
TitleCryo-EM structure of VX93 Fab in complex with GII.4 Norovirus P domain
Components
  • VP1
  • VX93 heavy chain
  • VX93 light chain
KeywordsVIRAL PROTEIN/Immune System / Norovirus / 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 speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsJo, G. / Ward, A.B.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Revision 1.1Sep 2, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
H: VX93 heavy chain
L: VX93 light chain
B: VP1
C: VX93 heavy chain
D: VX93 light chain


Theoretical massNumber of molelcules
Total (without water)121,7846
Polymers121,7846
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein VP1


Mass: 34215.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Production host: Escherichia coli (E. coli) / References: UniProt: K4LM89
#2: Antibody VX93 heavy chain


Mass: 14104.677 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody VX93 light chain


Mass: 12571.962 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: VX93 Fab in complex with GII.4 Norovirus P domain / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 190000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.03 sec. / Electron dose: 45 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3620

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
13cryoSPARC4.7.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 332242 / Symmetry type: POINT

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