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- PDB-9dpc: Structure of Fab 297 in complex with influenza H1N1 A/Victoria/48... -

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Basic information

Entry
Database: PDB / ID: 9dpc
TitleStructure of Fab 297 in complex with influenza H1N1 A/Victoria/4897/2022 neuraminidase
Components
  • Neuraminidase
  • Variable domain of the heavy chain of Fab 297
  • Variable domain of the light chain of Fab 297
KeywordsIMMUNE SYSTEM / Influenza / Neuraminidase / Antibody
Function / homology
Function and homology information


exo-alpha-sialidase / exo-alpha-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Sialidase, Influenza viruses A/B / Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsPholcharee, T. / Wu, N.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI165475 United States
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: J Exp Med / Year: 2025
Title: Identification of a seasonal influenza vaccine-induced broadly protective neuraminidase antibody.
Authors: Anders Madsen / Nisreen M A Okba / Tossapol Pholcharee / Hanover C Matz / Huibin Lv / Maria Ibanez Trullen / Julian Q Zhou / Jackson S Turner / Aaron J Schmitz / Fangjie Han / Stephen C ...Authors: Anders Madsen / Nisreen M A Okba / Tossapol Pholcharee / Hanover C Matz / Huibin Lv / Maria Ibanez Trullen / Julian Q Zhou / Jackson S Turner / Aaron J Schmitz / Fangjie Han / Stephen C Horvath / Sameer Kumar Malladi / Florian Krammer / Nicholas C Wu / Ali H Ellebedy /
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 ...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.
History
DepositionSep 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neuraminidase
B: Neuraminidase
C: Neuraminidase
D: Neuraminidase
H: Variable domain of the heavy chain of Fab 297
L: Variable domain of the light chain of Fab 297


Theoretical massNumber of molelcules
Total (without water)232,1246
Polymers232,1246
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
Neuraminidase


Mass: 51750.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Victoria/4897/2022 / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A6H1QYJ4, exo-alpha-sialidase
#2: Antibody Variable domain of the heavy chain of Fab 297


Mass: 13670.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi293F / Production host: Homo sapiens (human)
#3: Antibody Variable domain of the light chain of Fab 297


Mass: 11450.699 Da / Num. of mol.: 1
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: A complex of neuraminidase from influenza A A/Victoria/4897/2022 with human Fab 297
Type: COMPLEX
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab 297 was expressed recombinantly in Expi293F cells.
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was also mixed with octyl glucoside to 0.1% w/v of the detergent final concentration piror to applying on the grid.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 57.35 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
8PHENIXmodel refinement
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
13cryoSPARC4.53D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288521 / Symmetry type: POINT

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