9V3F | pdb_00009v3f

A neutralizing antibody targeting the F protein of NiV

PDB DOI: https://doi.org/10.2210/pdb9V3F/pdb
EM Map EMD-64754: EMDB EMDataResource

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Henipavirus nipahense, Homo sapiens
Expression System: Homo sapiens, Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2025-05-21 Released: 2026-04-08
Deposition Author(s): Wang, S., Rao, G., Cao, S., Gong, R.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Highly potent C-type nanoantibodies neutralize Nipah and Hendra viruses by cavity filling on fusion glycoprotein.

Wang, S., Rao, G., Zhang, X., Yao, Y., Chen, L., Chen, S., Zhang, H., Liu, H., Chen, M., Li, W., Cao, S., Chiu, S., Gong, R.

(2026) Nat Commun 17

PubMed: 42215462 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-026-73406-4
Primary Citation Related Structures:
9V3E, 9V3F

PubMed Abstract:
Nipah (NiV) and Hendra (HeV) viruses pose a serious threat, causing global outbreaks with high fatality rates. The fusion (F) glycoprotein, located on the viral surface, presents a conserved and promising neutralizing target. Here, we identify two C-type nanoantibodies (C-Nabs), 1A1-3-22 and 2A1-3-8, targeting F protein. 2A1-3-8 exhibits cross-reactivity against both viruses, whereas 1A1-3-22 shows specificity to NiV. The half-life-extended 2A1-3-8 provides 100% protection against NiV lethal challenge in female hamsters. Cryo-EM analysis reveals that 1A1-3-22 and 2A1-3-8 target similar funnel-like epitopes. Based on the unique "cavity-filling" mechanism, we engineered 2A1-3-8 to exhibit enhanced neutralizing activity and converted 1A1-3-22 from a NiV-specific antibody into a broad-spectrum one. In addition, the affinity-matured 2A1-3-8 clones exhibit broad binding activity against F proteins spanning both the Henipavirus and Parahenipavirus genera. Our study not only demonstrates the potential of C-Nabs for clinical application against henipaviruses, but also provides critical epitope information for the future design and engineering of antibodies and the development of other antivirals.

Organizational Affiliation

State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.

Macromolecule Content

Total Structure Weight: 214.16 kDa
Atom Count: 12,535
Modeled Residue Count: 1,596
Deposited Residue Count: 1,899
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, C [auth B], E [auth C]	502	Henipavirus nipahense	Mutation(s): 0
UniProt
Find proteins for Q9IH63 (Nipah virus) Explore Q9IH63 Go to UniProtKB: Q9IH63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9IH63
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C [auth B] Focus chain E [auth C]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type nanoantibody	B [auth E], D [auth F], F [auth G]	131	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth C]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B], M [auth C], N [auth C], O [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth C]