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- PDB-9hbp: Cryo-EM structure of the canine distemper virus tetrameric attach... -

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Basic information

Entry
Database: PDB / ID: 9hbp
TitleCryo-EM structure of the canine distemper virus tetrameric attachment H glycoprotein in complex with two different Nanobodies
Components
  • Hemagglutinin glycoprotein
  • Nanobody H7
  • Nanobody H9
KeywordsVIRAL PROTEIN / canine distemper virus / hemagglutinine / CDV / H-protein / Complex / Nanobody
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesMorbillivirus canis
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDjabeur, N. / Jeckelmann, J.M. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationCRSII5_183481 Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Protection against lethal canine distemper virus infection by a dual epitope-targeting synthetic antibody.
Authors: Melanie Scherer / Nadia Djabeur / Oliver Siering / Jean-Marc Jeckelmann / Marianne Wyss / Marina Cresci / Morgane Di Palma Subran / Rainer Riedl / Patrick Chames / Christian K Pfaller / ...Authors: Melanie Scherer / Nadia Djabeur / Oliver Siering / Jean-Marc Jeckelmann / Marianne Wyss / Marina Cresci / Morgane Di Palma Subran / Rainer Riedl / Patrick Chames / Christian K Pfaller / Bevan Sawatsky / Dimitrios Fotiadis / Philippe Plattet /
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 ...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.
History
DepositionNov 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin glycoprotein
B: Hemagglutinin glycoprotein
E: Nanobody H7
F: Nanobody H7
G: Nanobody H9
H: Nanobody H9
C: Hemagglutinin glycoprotein
D: Hemagglutinin glycoprotein
I: Nanobody H7
J: Nanobody H7
K: Nanobody H9
L: Nanobody H9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)382,64716
Polymers381,76212
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, SDS-PAGE
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Hemagglutinin glycoprotein


Mass: 68311.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morbillivirus canis / Strain: A75/17 / Cell line: expiCHO / Cell line (production host): expiCHO / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9QPQ8
#2: Antibody
Nanobody H7


Mass: 13326.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Antibody
Nanobody H9


Mass: 13802.476 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Purified CDV-solH in complex with Nb H7 and Nb H9COMPLEX#1-#30MULTIPLE SOURCES
2Hemagglutinin glycoproteinCOMPLEX#11RECOMBINANT
3Nanobodies NbH7 and NbH9COMPLEX#2-#31RECOMBINANTNanobodies NbH7 and NbH9 purified separatlely
Molecular weightValue: 0.3731 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Morbillivirus canis3052342A75/17
33Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Cricetulus griseus (Chinese hamster)10029expiCHO
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.6 / Details: 20 mM Tris-HCl, 100 mM NaCl, 0.25% OG (w/v)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-HCl1
2100 mMsodium chlorideNaCl1
38.55 mMOctyl glycosideC14H28O61
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified CDV-solH in complex with Nb H7 and Nb H9 in a molar ratio = 1/2.5/2.5
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K
Details: Blot Time: 4.5 sec Blot Force: -4 Drain Time: 0 Wait time: 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 9162
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.5particle selectioncrYOLO was used to automatically select particle images
2EPU3image acquisition
4Gctf1.6CTF correction
5cryoSPARC4CTF correction
8UCSF ChimeraX1.7model fitting
10PHENIX1.2model refinement
11RELION4initial Euler assignment
12cryoSPARC4.2final Euler assignment
13RELION4classification
14cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 304110
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 118721 / Algorithm: FOURIER SPACE / Num. of class averages: 3 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-IDSource nameType
17ZNY

7zny

A7ZNYA1PDBexperimental model
27ZNY

7zny

B7ZNYB1PDBexperimental model
37ZNY

7zny

C7ZNYC1PDBexperimental model
47ZNY

7zny

D7ZNYD1PDBexperimental model
5EAlphaFoldin silico model
6FAlphaFoldin silico model
7GAlphaFoldin silico model
8HAlphaFoldin silico model
9IAlphaFoldin silico model
10JAlphaFoldin silico model

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