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 9DPC | pdb_00009dpc

Structure of Fab 297 in complex with influenza H1N1 A/Victoria/4897/2022 neuraminidase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Identification of a seasonal influenza vaccine-induced broadly protective neuraminidase antibody.

Madsen, A., Okba, N.M.A., Pholcharee, T., Matz, H.C., Lv, H., Ibanez Trullen, M., Zhou, J.Q., Turner, J.S., Schmitz, A.J., Han, F., Horvath, S.C., Malladi, S.K., Krammer, F., Wu, N.C., Ellebedy, A.H.

(2025) J Exp Med 222

  • DOI: https://doi.org/10.1084/jem.20241930
  • Primary Citation Related Structures: 
    9DPC

  • PubMed Abstract: 

    Seasonal influenza viruses cause significant global illness and death annually, and the potential spillover of avian H5N1 poses a serious pandemic threat. Traditional influenza vaccines target the variable hemagglutinin (HA) protein, necessitating annual vaccine updates, while the slower-evolving neuraminidase (NA) presents a promising target for broader protection. We investigated the breadth of anti-NA B cell responses to seasonal influenza vaccination in humans. We screened plasmablast-derived monoclonal antibodies (mAbs) from three donors, identifying 11 clonally distinct NA mAbs from 268 vaccine-specific mAbs. Among these, mAb-297 showed exceptionally broad NA inhibition, effectively protecting mice against lethal doses of influenza A and B viruses, including H5N1. We show that mAb-297 targets a common binding motif in the conserved NA active site. Our findings show that while B cell responses against NA following conventional, egg-derived influenza vaccines are rare, inducing broadly protective NA antibodies through such vaccination remains feasible, highlighting the importance of improving NA immunogens to develop a more broadly protective influenza vaccine.


  • Organizational Affiliation: 
    • Influenza Centre, Department of Clinical Science, University of Bergen, Bergen, Norway.

Macromolecule Content 

  • Total Structure Weight: 232.12 kDa 
  • Atom Count: 13,370 
  • Modeled Residue Count: 1,777 
  • Deposited Residue Count: 2,108 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuraminidase
A, B, C, D
469Influenza A virusMutation(s): 0 
Gene Names: NA
EC: 3.2.1.18
UniProt
Find proteins for A0A6H1QYJ4 (Influenza A virus)
Explore A0A6H1QYJ4 
Go to UniProtKB:  A0A6H1QYJ4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6H1QYJ4
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Variable domain of the heavy chain of Fab 297E [auth H]126Homo sapiensMutation(s): 0 
Entity Groups
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Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Variable domain of the light chain of Fab 297F [auth L]106Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.5

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 StatesR01 AI165475
Howard Hughes Medical Institute (HHMI)United StatesEmerging Pathogens Initiative

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-04-09
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-14
    Changes: Data collection