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- EMDB-70808: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10... -

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Basic information

Entry
Database: EMDB / ID: EMD-70808
TitleStructure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Map data
Sample
  • Complex: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab hb420
    • Protein or peptide: Variable domain of the light chain of Fab HB420
KeywordsInfluenza / Neuraminidase / Antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
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: 2.16 Å
AuthorsLv H / Wu NC
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI)Emerging Pathogens Initiative United States
CitationJournal: Cell Host Microbe / Year: 2025
Title: Evolution of antibody cross-reactivity to influenza H5N1 neuraminidase from an N2-specific germline.
Authors: Huibin Lv / Yang Wei Huan / Qi Wen Teo / Chunke Chen / Tossapol Pholcharee / Akshita B Gopal / Madison R Ardagh / Jessica J Huang / Ruipeng Lei / Xin Chen / Yuanxin Sun / Yun Sang Tang / ...Authors: Huibin Lv / Yang Wei Huan / Qi Wen Teo / Chunke Chen / Tossapol Pholcharee / Akshita B Gopal / Madison R Ardagh / Jessica J Huang / Ruipeng Lei / Xin Chen / Yuanxin Sun / Yun Sang Tang / Arjun Mehta / Mateusz Szlembarski / Kevin J Mao / Emily X Ma / Lucas E Wittenborn / Meixuan Tong / Lucia A Rodriguez / Letianchu Wang / Chris K P Mok / Nicholas C Wu /
Abstract: The ongoing spread of highly pathogenic avian influenza H5N1 clade 2.3.4.4b virus in animals and its occasional spillover to humans have raised concerns about a potential H5N1 pandemic. Although ...The ongoing spread of highly pathogenic avian influenza H5N1 clade 2.3.4.4b virus in animals and its occasional spillover to humans have raised concerns about a potential H5N1 pandemic. Although recent studies have shown that pre-existing human antibodies can recognize H5N1 neuraminidase, the molecular basis of how this cross-reactivity develops remains poorly understood. In this study, we used a phage display antibody library derived from 245 healthy donors to isolate an antibody, HB420, that cross-reacts with neuraminidases of human H3N2 and avian H5N1 clade 2.3.4.4b viruses and confers protection in vivo. Cryogenic electron microscopy analysis reveals that HB420 targets the neuraminidase active site by mimicking sialic acid binding through a single Asp residue. Furthermore, the inferred germline of HB420 is N2 specific but acquires cross-reactivity to H5N1 neuraminidase through somatic hypermutation. Overall, our findings provide insights into how neuraminidase antibody evolves breadth, which has important implications for the development of broadly protective influenza vaccines.
History
DepositionMay 25, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70808.png

Downloads & links

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Map

FileDownload / File: emd_70808.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 380.88 Å		1.06 Å/pix.
x 360 pix.
= 380.88 Å		1.06 Å/pix.
x 360 pix.
= 380.88 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.095
Minimum - Maximum-0.0017491005 - 1.6169193
Average (Standard dev.)0.0007444206 (±0.018703492)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
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_70808_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_70808_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10...

EntireName: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Components
  • Complex: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
    • Protein or peptide: Neuraminidase
    • Protein or peptide: Variable domain of the heavy chain of Fab hb420
    • Protein or peptide: Variable domain of the light chain of Fab HB420

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Supramolecule #1: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10...

SupramoleculeName: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab HB420 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
Molecular weightTheoretical: 42.767715 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ...String:
AEYRNWSKPQ CNITGFAPFS KDNSIRLSAG GDIWVTREPY VSCDPDKCYQ FALGQGTTLN NGHSNDTVHD RTPYRTLLMN ELGVPFHLG TKQVCIAWSS SSCHDGKAWL HVCVTGDDEN ATASFIYNGR LVDSIGSWSK KILRTQESEC VCINGTCTVV M TDGSASGK ADTKILFIEE GKIVHTSPLS GSAQHVEECS CYPRYPGVRC VCRDNWKGSN RPIVDINVKD YSIVSSYVCS GL VGDTPRK NDSSSSSHCL DPNNEEGGHG VKGWAFDDGN DVWMGRTISE KLRSGYETFK VIEGWSKPNS KLQINRQVIV DRG NRSGYS GIFSVEGKSC INRCFYVELI RGRKQETEVL WTSNSIVVFC GTSGTYGTGS WPDGADINLM PI

UniProtKB: Neuraminidase

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Macromolecule #2: Variable domain of the heavy chain of Fab hb420

MacromoleculeName: Variable domain of the heavy chain of Fab hb420 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.544985 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGAE VKKPGSSVKV SCMASGGSFG SYGFSWVRQA PGQGLEWMGG IIPLFDTPNY AQKFQGRVTI TADASTSTVY MELSSLRSE DTAVYYCARD SLPYGDQNYY YGMHVWGQGT TVTVSS

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Macromolecule #3: Variable domain of the light chain of Fab HB420

MacromoleculeName: Variable domain of the light chain of Fab HB420 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.460441 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSALTQPASL SGSPGQSITI SCSGSSSDIG DYNYVSWYQQ HPGKAPKLII YDVTNRPSGV SDRLSGSKSG TTASLTISGL QAEDEADYY CSSYGGNYNL VFGGGTKLTV L

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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
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: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 355667
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)

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