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- PDB-9osr: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10... -

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Basic information

Entry
Database: PDB / ID: 9osr
TitleStructure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Components
  • Neuraminidase
  • Variable domain of the heavy chain of Fab hb420
  • Variable domain of the light chain of Fab HB420
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Influenza / 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 speciesInfluenza A virus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsLv, H. / Wu, N.C.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Oct 29, 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_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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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
J: Variable domain of the heavy chain of Fab hb420
H: Variable domain of the heavy chain of Fab hb420
N: Variable domain of the light chain of Fab HB420
K: Variable domain of the heavy chain of Fab hb420
L: Variable domain of the light chain of Fab HB420
R: Variable domain of the light chain of Fab HB420
I: Variable domain of the heavy chain of Fab hb420
M: Variable domain of the light chain of Fab HB420


Theoretical massNumber of molelcules
Total (without water)271,09312
Polymers271,09312
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Neuraminidase


Mass: 42767.715 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Gene: NA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8AZ87, exo-alpha-sialidase
#2: Antibody
Variable domain of the heavy chain of Fab hb420


Mass: 13544.985 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody
Variable domain of the light chain of Fab HB420


Mass: 11460.441 Da / Num. of mol.: 4
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: Structure of Fab HB420 in complex with influenza H3N2 A/Moscow/10/1999 neuraminidase
Type: COMPLEX
Details: Neuraminidase was expressed recombinantly in SF9 cells. Fab HB420 was expressed recombinantly in Expi293F cells.
Entity ID: all / Source: MULTIPLE SOURCES
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.
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
10cryoSPARC4.5initial Euler assignment
11cryoSPARC4.5final Euler assignment
13cryoSPARC4.53D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355667 / Symmetry type: POINT

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