9HBP | pdb_00009hbp

Cryo-EM structure of the canine distemper virus tetrameric attachment H glycoprotein in complex with two different Nanobodies

• PDB DOI: https://doi.org/10.2210/pdb9HBP/pdb
• EM Map EMD-52024: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Morbillivirus canis, Lama glama
• Expression System: Cricetulus griseus, Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-07 Released: 2026-01-21 
• Deposition Author(s): Djabeur, N., Jeckelmann, J.M., Fotiadis, D.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Protection against lethal canine distemper virus infection by a dual epitope-targeting synthetic antibody.

Scherer, M., Djabeur, N., Siering, O., Jeckelmann, J.M., Wyss, M., Cresci, M., Di Palma Subran, M., Riedl, R., Chames, P., Pfaller, C.K., Sawatsky, B., Fotiadis, D., Plattet, P.

(2026) Nat Commun 17: 103-103

• PubMed: 41501035 
• DOI: https://doi.org/10.1038/s41467-025-67600-z
• Primary Citation of Related Structures:  
  9HBP


• PubMed Abstract: 
  

  Despite vaccine availability, the morbilliviruses measles virus and canine distemper virus (CDV) are still causing major health impairments in human and animal populations. Here, we identified two potent, neutralizing single domain antibodies directed against the tetrameric receptor binding (H) protein of CDV. Structural analyses spotlighted two vulnerable sites within the H protein. While the first overlaps with the receptor binding site, the second encompasses amino acid residues of two protomers located at the distal dimeric head interface, which supports distinct mechanisms of neutralization. Upon application of an engineered tetravalent and biparatopic antibody, ferrets were protected at a remarkably low antibody dose (1 mg/kg) administered intra-peritoneally on days 3 and 7 post-exposure of a lethal CDV challenge. Collectively, this study spotlights the power of integrating multiple mechanisms of neutralization in a single format and provides a roadmap to design next-generation therapeutics against morbilliviral infections as well as other infectious pathogens.

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Organizational Affiliation: 
• Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland.
Institute of Medical Microbiology, University of Zurich, Zürich, Switzerland.
Institute of Biochemistry and Molecular Medicine, Medical Faculty, University of Bern, Bern, Switzerland.
Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany.
Aix-Marseille Université, CNRS, INSERM, Institute Paoli-Calmettes, CRCM, Marseille, France.
Competence Center for Drug Discovery, ZHAW Zurich University of Applied Sciences, Institute of Chemistry and Biotechnology, Wädenswil, Switzerland.
Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Rochester, MN, USA.
Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA.
Division of Veterinary Medicine, Paul-Ehrlich-Institute, Langen, Germany. [e-mail].
Institute of Biochemistry and Molecular Medicine, Medical Faculty, University of Bern, Bern, Switzerland. [e-mail].
Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland. [e-mail].
Division of Neurological Sciences, Vetsuisse Faculty, University of Bern, Bern, Switzerland. [e-mail].
Multidisciplinary Center for Infectious Diseases (MCID), University of Bern, Bern, Switzerland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A4B4C4 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A8B4 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 382.65 kDa 
• Atom Count: 20,375 
• Modeled Residue Count: 2,610 
• Deposited Residue Count: 3,432 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemagglutinin glycoprotein	A, B, G [auth C], H [auth D]	607	Morbillivirus canis	Mutation(s): 0
UniProt
Find proteins for Q9QPQ8 (Morbillivirus canis) Explore Q9QPQ8  Go to UniProtKB:  Q9QPQ8
Glycosylation
Glycosylation Sites: 1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H7	C [auth E], D [auth F], I, J	124	Lama glama	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody H9	E [auth G], F [auth H], K, L	127	Lama glama	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	M [auth A], N [auth B], O [auth C], P [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20
RECONSTRUCTION	cryoSPARC	4.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Djabeur, N., Jeckelmann, J.M., Fotiadis, D.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	CRSII5_183481

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release