8Z4E | pdb_00008z4e

Structure of human 18_14D scFv and 1G01 scFv in complex with influenza virus neuraminidase from A/Yunan/DQ001/2016 (H5N6)

• PDB DOI: https://doi.org/10.2210/pdb8Z4E/pdb
• EM Map EMD-39762: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Influenza A virus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2024-04-17 Released: 2025-01-22 
• Deposition Author(s): Wang, M., Peng, Q., Gao, Y., Shi, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A human monoclonal antibody targeting the monomeric N6 neuraminidase confers protection against avian H5N6 influenza virus infection.

Wang, M., Gao, Y., Shen, C., Yang, W., Peng, Q., Cheng, J., Shen, H.M., Yang, Y., Gao, G.F., Shi, Y.

(2024) Nat Commun 15: 8871-8871

• PubMed: 39402031 
• DOI: https://doi.org/10.1038/s41467-024-53301-6
• Primary Citation of Related Structures:  
  8Z4E


• PubMed Abstract: 
  

  The influenza neuraminidase (NA) is a potential target for the development of a next-generation influenza vaccine, but its antigenicity is not well understood. Here, we isolate an anti-N6 human monoclonal antibody, named 18_14D, from an H5N6 avian influenza virus (AIV) infected patient. The antibody weakly inhibits enzymatic activity but confers protection in female mice, mainly via ADCC function. The cryo-EM structure shows that 18_14D binds to a unique epitope on the lateral surface of the N6 tetramer, preventing the formation of tightly closed NA tetramers. These findings contribute to the molecular understanding of protective immune responses to NA of AIVs in humans and open an avenue for the rational design of NA-based vaccines.

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Organizational Affiliation: 
• CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China.
Faculty of Health Sciences, University of Macau, Macau, China.
BSL-3 Laboratory (Guangdong), Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health; Southern Medical University, Guangzhou, China.
Medical School, University of Chinese Academy of Sciences, Beijing, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].
Medical School, University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Beijing Life Science Academy, Beijing, China. [e-mail].
CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China. [e-mail].
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen, China. [e-mail].
Medical School, University of Chinese Academy of Sciences, Beijing, China. [e-mail].
Beijing Life Science Academy, Beijing, China. [e-mail].
Health Science Center, Ningbo University, Ningbo, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 139.11 kDa 
• Atom Count: 6,327 
• Modeled Residue Count: 821 
• Deposited Residue Count: 1,279 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuraminidase	A	379	Influenza A virus	Mutation(s): 0  Gene Names: NA EC: 3.2.1.18
UniProt
Find proteins for A0A884WLQ3 (Influenza A virus) Explore A0A884WLQ3  Go to UniProtKB:  A0A884WLQ3
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 18_14D scFv	B	216	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 18_14D scFv	C	236	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of 1G01 scFv	D [auth E]	232	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of 1G01 scFv	E [auth F]	216	Homo sapiens	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA (Subject of Investigation/LOI)	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Wang, M., Peng, Q., Gao, Y., Shi, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32192452

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release