[English] 日本語
Yorodumi
- EMDB-52021: Cryo-EM focused refined map of the canine distemper virus dimer I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52021
TitleCryo-EM focused refined map of the canine distemper virus dimer II region of the tetrameric attachment H glycoprotein in complex with two different Nanobodies
Map dataFocused refinement density map - dimer II: 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 H7 H9
Keywordscanine distemper virus / hemagglutinine / CDV / H-protein / Complex / Nanobody / VIRAL PROTEIN
Biological speciesMorbillivirus canis / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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

-
Structure visualization

Supplemental images

emd_52021.png

Downloads & links

-
Map

FileDownload / File: emd_52021.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused refinement density map - dimer II: 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: 0.244
Minimum - Maximum-3.5091534 - 4.4141407
Average (Standard dev.)0.0021815775 (±0.031860005)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: Focused refinement density Half-map A (dimer II)

Fileemd_52021_half_map_1.map
AnnotationFocused refinement density Half-map A (dimer II)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Focused refinement density Half-map B (dimer II)

Fileemd_52021_half_map_2.map
AnnotationFocused refinement density Half-map B (dimer II)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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 H7 H9

-
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

-
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

-
Supramolecule #3: Nanobodies H7 H9

SupramoleculeName: Nanobodies H7 H9 / type: complex / ID: 3 / Parent: 1 / Details: seperately purified
Source (natural)Organism: Lama glama (llama)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 3.152Tris-HClTris(hydroxymethyl)aminomethane hydrochloride
100.0 9NaClsodium chloride
8.55 2.5C14H28O6Octyl 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

-
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

+
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: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2)
Details: Focused refinement was performed by applying a mask around the dimer II region to enhance resolution in this specific area.
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more