8VKX | pdb_00008vkx

VX22 bound to GII.4 P domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 
    0.272 (Depositor), 0.271 (DCC) 
  • R-Value Work: 
    0.245 (Depositor), 0.243 (DCC) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Broadly neutralizing antibodies targeting pandemic GII.4 variants or seven GII genotypes of human norovirus.

Park, J.Lindesmith, L.C.Olia, A.S.Costantini, V.P.Brewer-Jensen, P.D.Mallory, M.L.Kelley, C.E.Satterwhite, E.Longo, V.Tsybovsky, Y.Stephens, T.Marchioni, J.Martins, C.A.Huang, Y.Chaudhary, R.Zweigart, M.May, S.R.Reyes, Y.Flitter, B.Vinje, J.Tucker, S.N.Ippolito, G.C.Lavinder, J.J.Snijder, J.Kwong, P.D.Georgiou, G.Baric, R.S.

(2025) Sci Transl Med 17: eads8214-eads8214

  • DOI: https://doi.org/10.1126/scitranslmed.ads8214
  • Primary Citation of Related Structures:  
    8VKX

  • PubMed Abstract: 

    Human norovirus causes more than 700 million illnesses annually. Extensive genetic diversity and a paucity of information on conserved neutralizing epitopes pose major obstacles to the design of broadly protective norovirus immunogens. Here, we used high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS)-driven proteomics to quantitatively characterize the circulating serum IgG repertoire before and after immunization with an experimental monovalent norovirus GII.4 VP1 capsid-encoding adenoviral vaccine. Two participants were specifically selected on the basis of the breadth of serum neutralization responses either across GII.4 variants (participant A) or across GII genotypes (participant B). In participant A, vaccination back-boosted highly abundant serum antibody clonotypes targeting epitopes conserved among rapidly evolving GII.4 variants spanning from a strain identified in 1987 to a strain identified in 2019. In participant B, we identified a recall response consisting of broadly neutralizing monoclonal antibodies with remarkable cross-GII ligand-binding blockade (blocking ≥ seven GII genotypes) and virus neutralization breadth. The cocrystal structure of one of these antibodies, VX22, in complex with the VP1 capsid protruding (P) domain revealed a highly conserved epitope (residues 479 to 484 and 509 to 513) within two lateral loops of the P1 subdomain. Antibody evolutionary trajectory analysis further revealed that VX22 had originally evolved from an early heterologous infection, likely by a GII.12 strain. Together, our study demonstrates that norovirus human monoclonal antibodies with broad GII.4 potency and cross-GII breadth can be boosted in serum after immunization with an adenoviral vector-based vaccine, findings that may guide the design of immunogens for broadly protective norovirus vaccines.


  • Organizational Affiliation
    • Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
VX22 heavy chainA [auth H]235Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
VX22 light chainB [auth L]216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
VP1C [auth A]306Norovirus Hu/GII.4/Sydney/NSW0514/2012/AUMutation(s): 0 
UniProt
Find proteins for K4LM89 (Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU)
Explore K4LM89 
Go to UniProtKB:  K4LM89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK4LM89
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free:  0.272 (Depositor), 0.271 (DCC) 
  • R-Value Work:  0.245 (Depositor), 0.243 (DCC) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.326α = 90
b = 148.98β = 90
c = 148.872γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-19
    Type: Initial release
  • Version 1.1: 2025-09-03
    Changes: Database references