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- EMDB-47102: Structure of Fab 297 in complex with influenza H1N1 A/Victoria/48... -

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Basic information

Entry
Database: EMDB / ID: EMD-47102
TitleStructure of Fab 297 in complex with influenza H1N1 A/Victoria/4897/2022 neuraminidase
Map data
Sample
  • Complex: A complex of neuraminidase from influenza A A/Victoria/4897/2022 with human Fab 297
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab 297
    • Protein or peptide: Variable domain of the light chain of Fab 297
KeywordsInfluenza / Neuraminidase / Antibody / IMMUNE SYSTEM
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 speciesHomo sapiens (human) / Influenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsPholcharee T / Wu NC
Funding support United States, 2 items
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, 2024-
Header (metadata) releaseMar 19, 2025-
Map releaseMar 19, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47102.png

Downloads & links

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Map

FileDownload / File: emd_47102.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å		0.53 Å/pix.
x 720 pix.
= 380.88 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.529 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.058
Minimum - Maximum-0.0018118906 - 1.7350239
Average (Standard dev.)0.0005213594 (±0.017198224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 380.87997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47102_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47102_half_map_2.map
Projections & Slices
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Sample components

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Entire : A complex of neuraminidase from influenza A A/Victoria/4897/2022 ...

EntireName: A complex of neuraminidase from influenza A A/Victoria/4897/2022 with human Fab 297
Components
  • Complex: A complex of neuraminidase from influenza A A/Victoria/4897/2022 with human Fab 297
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab 297
    • Protein or peptide: Variable domain of the light chain of Fab 297

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Supramolecule #1: A complex of neuraminidase from influenza A A/Victoria/4897/2022 ...

SupramoleculeName: A complex of neuraminidase from influenza A A/Victoria/4897/2022 with human Fab 297
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab 297 was expressed recombinantly in Expi293F cells.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Neuraminidase

MacromoleculeName: Neuraminidase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: exo-alpha-sialidase
Source (natural)Organism: Influenza A virus / Strain: A/Victoria/4897/2022
Molecular weightTheoretical: 51.750938 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNPNQKIITI GSICMTIGTA NLILQIGNII SIWVSHSIQI GNQSQIETCD KSVITYENNT WVNQTFVNIS NTNSAARQSV ASVKLAGNS SLCPVSGWAI YSKDNSVRIG SKGDVFVIRE PFISCSPLEC RTFFLTQGAL LNDKHSNGTI KDRSPYRTLM S CPIGEVPS ...String:
MNPNQKIITI GSICMTIGTA NLILQIGNII SIWVSHSIQI GNQSQIETCD KSVITYENNT WVNQTFVNIS NTNSAARQSV ASVKLAGNS SLCPVSGWAI YSKDNSVRIG SKGDVFVIRE PFISCSPLEC RTFFLTQGAL LNDKHSNGTI KDRSPYRTLM S CPIGEVPS PYNSRFESVA WSASACHDGT NWLTIGISGP DSGAVAVLKY NGIITDTIKS WRNKILRTQE SECACVNGSC FT IMTDGPS DGQASYKIFR IEKGKIIKSV EMKAPNYHYE ECSCYPDSSE ITCVCRDNWH GSNRPWVSFN QNLEYQMGYI CSG VFGDNP RPNDKTGSCG PVSSNGANGV KGFSFKYGNG VWIGRTKSIS SRKGFEMIWD PNGWTETDNK FSKKQDIVGI NEWS GYSGS FVQHPELTGL NCIRPCFWVE LIRGRPEENT IWTSGSSISF CGVDSDIMGW SWPDGAELPF TIDN

UniProtKB: Neuraminidase

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Macromolecule #2: Variable domain of the heavy chain of Fab 297

MacromoleculeName: Variable domain of the heavy chain of Fab 297 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.670041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKASGDTFS SYAISWVRQA PGQGLEWMGG IIPFLGTTNY AQKFQGRVTI TTDESSTTAD MELSSLRSE DTAVYYCATS YSGYDRIQYY YSGMDVWGQG TTVTVSS

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Macromolecule #3: Variable domain of the light chain of Fab 297

MacromoleculeName: Variable domain of the light chain of Fab 297 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.450699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVRDRVT ITCRSSQSVF TYLNWYQQKP GKAPKLLISA ASTLQSGVPS RFSGSGSGTD FTLTINSLQP EDFATYYCQ QSFSTPLTFG GGTKVDI

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl, 100 mM NaCl, 10 mM CaCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK III
DetailsThe sample was also mixed with octyl glucoside to 0.1% w/v of the detergent final concentration piror to applying on the grid.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.35 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: Initial model was built directly into the map using automated model building algorithm ModelAngelo (DOI: 10.1038/s41586-024-07215-4)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 288521
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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