9BOF | pdb_00009bof

16E10 Fab bound to norovirus GI.1 P domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A broadly protective human antibody for GI genogroup noroviruses.

Rimkute, I.Olia, A.S.Suleiman, M.Woods, K.D.Bylund, T.Morano, N.C.Tully, E.S.Verardi, R.Bao, S.Beddall, M.H.Chaimongkol, N.Donaldson, M.M.Du, R.Dulan, C.N.M.Gorman, J.Henry, A.R.Schramm, C.A.Sosnovtsev, S.V.Stephens, T.Todd, J.P.Tsybovsky, Y.Douek, D.C.Green, K.Y.Rawi, R.Shapiro, L.Zhou, T.Kwong, P.D.Roederer, M.

(2025) Nat Microbiol 10: 1227-1239

  • DOI: https://doi.org/10.1038/s41564-025-01952-6
  • Primary Citation of Related Structures:  
    9BOF

  • PubMed Abstract: 

    Noroviruses infect millions each year, and while effective countermeasures are eagerly sought, none have been reported for the GI genogroup, first described more than 50 years ago. Here, to provide insight into GI norovirus neutralization, we isolated a broad GI antibody, 16E10, from a human blood donor and showed it neutralizes noroviruses in human enteroid cultures and abrogates or reduces infection in rhesus macaques. The cryogenic electron microscopy reconstruction of 16E10 with a norovirus protruding-domain dimer at 2.56-Å resolution reveals an exceptionally large binding surface, overlapping an antibody supersite, distal from host receptor-binding or cofactor-binding sites. Cryogenic electron microscopy reconstructions with virus-like particles (VLPs) showed that 16E10 disrupts protruding domains on the VLP surface and disassembles VLPs, altering viral organization required for avidity. While its epitope was generally conserved, 16E10 recognized multiple sequence-divergent residues, binding to which was enabled by corresponding cavities in the 16E10-norovirus interface. Broad recognition of noroviruses can thus incorporate sequence-divergent residues, through a cavity-based mechanism of diversity tolerance.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein VP1
A, B
294NorovirusMutation(s): 0 
Gene Names: ORF2
UniProt
Find proteins for Q83884 (Norovirus (strain Human/NoV/United States/Norwalk/1968/GI))
Explore Q83884 
Go to UniProtKB:  Q83884
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ83884
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
16E10 Light ChainC,
F [auth H]
219Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
16E10 Heavy ChainD [auth E],
E [auth G]
231Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.61 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2025-04-09
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection
  • Version 1.2: 2025-10-22
    Changes: Data collection, Database references