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- EMDB-52020: Cryo-EM consensus map of the canine distemper virus tetrameric at... -

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Basic information

Entry
Database: EMDB / ID: EMD-52020
TitleCryo-EM consensus map of the canine distemper virus tetrameric attachment H glycoprotein in complex with two different Nanobodies
Map dataConsensus density map: receptor-binding tetrameric attachment (H)-protein of canine distemper virus (CDV) bound with 2 nanobodies, designated NbH7 and NbH9
Sample
  • Complex: Purified CDV-solH in complex with Nb H7 and Nb H9
    • Complex: Hemagglutinin glycoprotein
    • Complex: Nanobodies NbH7 and NbH9
Keywordscanine distemper virus / hemagglutinine / CDV / H-protein / Complex / Nanobody / VIRAL PROTEIN
Biological speciesMorbillivirus canis / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsDjabeur N / Jeckelmann JM / Fotiadis D
Funding support Switzerland, 1 items
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, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52020.png

Downloads & links

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Map

FileDownload / File: emd_52020.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus density map: receptor-binding tetrameric attachment (H)-protein of canine distemper virus (CDV) bound with 2 nanobodies, designated NbH7 and NbH9
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 351.84 Å		0.73 Å/pix.
x 480 pix.
= 351.84 Å		0.73 Å/pix.
x 480 pix.
= 351.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.733 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.142
Minimum - Maximum-0.12917505 - 0.44385394
Average (Standard dev.)0.002145696 (±0.019051671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 351.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Consensus half-density map A

Fileemd_52020_half_map_1.map
AnnotationConsensus half-density map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Consensus half-density map B

Fileemd_52020_half_map_2.map
AnnotationConsensus half-density map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Purified CDV-solH in complex with Nb H7 and Nb H9

EntireName: Purified CDV-solH in complex with Nb H7 and Nb H9
Components
  • Complex: Purified CDV-solH in complex with Nb H7 and Nb H9
    • Complex: Hemagglutinin glycoprotein
    • Complex: Nanobodies NbH7 and NbH9

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Supramolecule #1: Purified CDV-solH in complex with Nb H7 and Nb H9

SupramoleculeName: Purified CDV-solH in complex with Nb H7 and Nb H9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Molecular weightTheoretical: 373.1 KDa

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Supramolecule #2: Hemagglutinin glycoprotein

SupramoleculeName: Hemagglutinin glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #7-#8
Source (natural)Organism: Morbillivirus canis / Strain: A75/17

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Supramolecule #3: Nanobodies NbH7 and NbH9

SupramoleculeName: Nanobodies NbH7 and NbH9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6, #9-#12 / Details: Nanobodies NbH7 and NbH9 purified separatlely
Source (natural)Organism: Lama glama (llama)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris(hydroxymethyl)aminomethane hydrochloride
100.0 mMNaClsodium chloride
0.25 %C14H28O6Octyl glycoside

Details: 20 mM Tris-HCl, 100 mM NaCl, 0.25% OG (w/v)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: Blot Time: 4.5 sec Blot Force: -4 Drain Time: 0 Wait time: 0.
DetailsPurified CDV-solH in complex with Nb H7 and Nb H9 in a molar ratio = 1/2.5/2.5

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 9162 / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 304110
CTF correctionSoftware: (Name: Gctf (ver. 1.6), cryoSPARC (ver. 4)) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7zny

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 118721
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2)
Final 3D classificationNumber classes: 7 / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7zny

chain_id: A, source_name: PDB, initial_model_type: experimental model

7zny

chain_id: B, source_name: PDB, initial_model_type: experimental model

7zny

chain_id: C, source_name: PDB, initial_model_type: experimental model

7zny

chain_id: D, source_name: PDB, initial_model_type: experimental model
chain_id: E, source_name: AlphaFold, initial_model_type: in silico model
chain_id: F, source_name: AlphaFold, initial_model_type: in silico model
chain_id: G, source_name: AlphaFold, initial_model_type: in silico model
chain_id: H, source_name: AlphaFold, initial_model_type: in silico model
chain_id: I, source_name: AlphaFold, initial_model_type: in silico model
chain_id: J, source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: RIGID BODY FIT

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