9B9E | pdb_00009b9e

Prefusion F glycoprotein ectodomain of Nipah virus ectodomain in complex with DS90 nanobody

PDB DOI: https://doi.org/10.2210/pdb9B9E/pdb
EM Map EMD-44380: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Henipavirus nipahense, Vicugna pacos
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2024-04-01 Released: 2025-06-04
Deposition Author(s): Low, Y.S., Isaacs, A., Modhiran, N., Watterson, D.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

A nanobody-based therapeutic targeting Nipah virus limits viral escape.

Isaacs, A., Nieto, G.V., Zhang, X., Modhiran, N., Barr, J., Thakur, N., Low, Y.S., Parry, R.H., Barnes, J.B., Jara, R., Himelreichs, J., Yao, Y., Deride, C., Barthou-Gatica, B., Salinas-Rebolledo, C., Ehrenfeld, P., Hen, J.J., Hayes, N., Paramitha, D., Morgan, M.S., McMillan, C.L.D., Jones, M.L., Munro, T.P., Khromykh, A.A., Reading, P.C., Young, P.R., Chappell, K.J., Shi, Y., Bailey, D., Marsh, G.A., Chiu, S., Rojas-Fernandez, A., Watterson, D.

(2025) Nat Struct Mol Biol 32: 1920-1931

PubMed: 40629166 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41594-025-01598-2
Primary Citation Related Structures:
9B9E

PubMed Abstract:
Nipah virus (NiV) and Hendra virus (HeV) are highly pathogenic henipaviruses without approved human vaccines or therapies. Here, we report on a highly potent bispecific therapeutic that combines an anti-fusion glycoprotein nanobody with an anti-receptor-binding glycoprotein (RBP) antibody to deliver a dual-targeting biologic that is resistant to viral escape. We show that the nanobody, DS90, engages a unique, conserved site within the fusion glycoprotein of NiV and HeV and provides neutralization and complete protection from NiV disease. Bispecific engineering of DS90 with the anti-RBP monoclonal antibody m102.4 results in neutralization, elimination of viral escape and superior protection from NiV disease compared to leading monovalent approaches. These findings carry implications for the development of cross-neutralizing immunotherapies that limit the emergence of henipaviral escape mutants.

Organizational Affiliation

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia.

Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland, Australia.

Healthcare Science Faculty, Universidad San Sebastián, Valdivia, Chile.

Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.

CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.

CSIRO, Health and Biosecurity, Australian Centre for Disease Preparedness, Geelong, Victoria, Australia.

The Pirbright Institute, Surrey, UK.

Nuffield Department of Medicine, University of Oxford, Oxford, UK.

WHO Collaborating Centre for Reference and Research on Influenza, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.

Institute of Biochemistry and Microbiology, Faculty of Sciences, Universidad Austral de Chile, Valdivia, Chile.

Laboratory of Cellular Pathology, Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.

The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.

CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.

Department of Laboratory Medicine, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Heifei, China. qiux@ustc.edu.cn.

Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Hefei, China. qiux@ustc.edu.cn.

Institute of Medicine, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile. alejandro.rojas@uach.cl.

School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia. d.watterson@uq.edu.au.

Australian Infectious Disease Research Centre, Global Virus Network Centre of Excellence, Brisbane, Queensland, Australia. d.watterson@uq.edu.au.

Macromolecule Content

Total Structure Weight: 193.77 kDa
Atom Count: 13,542
Modeled Residue Count: 1,740
Deposited Residue Count: 1,743
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C	457	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: 4	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DS90 nanobody	D, E, F	124	Vicugna pacos	Mutation(s): 0

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 A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [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 A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [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 A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth B] G [auth A], H [auth A], I [auth A], J [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth C], P [auth C], Q [auth C], R [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 A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C]