9TQ8 | pdb_00009tq8

Neuraminidase NA isolated from the H1N1 strain A/Victoria/2570/2019 propagated in eggs in complex with zanamivir

PDB DOI: https://doi.org/10.2210/pdb9TQ8/pdb
EM Map EMD-56127: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Influenza A virus (A/(H1N1))
Mutation(s): No

Deposited: 2025-12-19 Released: 2026-06-10
Deposition Author(s): Borowska, A., Kang, H., Slotboom, D.J., Daniels, R.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

INAAC: An affinity chromatography strategy enabling characterization and quantification of influenza neuraminidase antigens in vaccines.

Kang, H., Borowska, A.M., Kanai, T., Gao, J., Yu, H., Chen, X., Gorman, J., Slotboom, D.J., Daniels, R.

(2026) J Biol Chem 302: 113138-113138

PubMed: 42119981 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jbc.2026.113138
Primary Citation Related Structures:
9TQ7, 9TQ8

PubMed Abstract:
Seasonal influenza vaccines are commonly produced using viruses containing hemagglutinin (HA) and neuraminidase (NA) antigens from recommended strains. However, NA amounts are not monitored due to lack of strategies for isolating NA reference antigens from viruses, limiting the ability to evaluate any contributions from NA for more than 50 years. Here, we developed an influenza neuraminidase active-site affinity chromatography (INAAC) strategy that uses an active-site binding antibody to isolate functional NAs from influenza A and B vaccine strains. INAAC recovered 20 to 60% of detergent-solubilized NA activity from vaccine viruses and recombinant sources, with CaCl ₂ elution proving most effective. ELISA results with the isolated NA from the H1N1 strain and recombinant full-length N1 showed that a commercial vaccine contains functional N1 and H1 at a ratio of ∼1:10. Structure determination of the isolated N1 by cryo-electron microscopy confirmed the native tetrameric conformation and provided insight into the stalk conformation of a virus-derived NA. Finally, comparative analyses of NAs isolated from recent egg-propagated vaccine strains (H1N1, H3N2, and type B) revealed a unique proteolytic susceptibility of type B NA and strain-specific differences in sialic acid affinities and catalytic rates. These results demonstrate that INAAC supports multiple applications from NA structural analysis to producing NA vaccine antigens and reference standards, addressing longstanding challenges for incorporating NA into influenza vaccine development and quality control.

Organizational Affiliation

Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA.

Macromolecule Content

Total Structure Weight: 210.79 kDa
Atom Count: 12,244
Modeled Residue Count: 1,548
Deposited Residue Count: 1,876
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A, B, C, D	469	Influenza A virus (A/(H1N1))	Mutation(s): 0 EC: 3.2.1.18
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZMR (Subject of Investigation/LOI) Query on ZMR Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], O [auth C], T [auth D]	ZANAMIVIR C₁₂ H₂₀ N₄ O₇ ARAIBEBZBOPLMB-UFGQHTETSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], P [auth C], Q [auth C], R [auth C], U [auth D], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D]
CA (Subject of Investigation/LOI) Query on CA Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain S [auth C] SDF format, chain N [auth B] SDF format, chain I [auth A] MOL2 format, chain X [auth D] MOL2 format, chain S [auth C] MOL2 format, chain N [auth B] MOL2 format, chain I [auth A] mmCIF format, chain X [auth D] mmCIF format, chain S [auth C] mmCIF format, chain N [auth B] mmCIF format, chain I [auth A]	I [auth A], N [auth B], S [auth C], X [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain X [auth D] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain S [auth C] Focus chain X [auth D]