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- PDB-7zny: Cryo-EM structure of the canine distemper virus tetrameric attach... -

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Basic information

Entry
Database: PDB / ID: 7zny
TitleCryo-EM structure of the canine distemper virus tetrameric attachment glycoprotein
ComponentsHemagglutinin glycoprotein
KeywordsVIRAL PROTEIN / canine distemper virus / morbillivirus cell entry / receptor-binding protein H / soluble H ectodomain
Function / homology
Function and homology information


host cell membrane / host cell surface receptor binding / symbiont entry into host cell / viral envelope / 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 speciesCanine morbillivirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
Model detailstetramer, four heads, one neck, ectodomain, viral protein
AuthorsKalbermatter, D. / Jeckelmann, J.-M. / Wyss, M. / Plattet, P. / Fotiadis, D.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSinergia, Ref. No. 183481 Switzerland
CitationJournal: Proc Natl Acad Sci U S A / Year: 2023
Title: Structure and supramolecular organization of the canine distemper virus attachment glycoprotein.
Authors: David Kalbermatter / Jean-Marc Jeckelmann / Marianne Wyss / Neeta Shrestha / Dimanthi Pliatsika / Rainer Riedl / Thomas Lemmin / Philippe Plattet / Dimitrios Fotiadis /
Abstract: Canine distemper virus (CDV) is an enveloped RNA morbillivirus that triggers respiratory, enteric, and high incidence of severe neurological disorders. CDV induces devastating outbreaks in wild and ...Canine distemper virus (CDV) is an enveloped RNA morbillivirus that triggers respiratory, enteric, and high incidence of severe neurological disorders. CDV induces devastating outbreaks in wild and endangered animals as well as in domestic dogs in countries associated with suboptimal vaccination programs. The receptor-binding tetrameric attachment (H)-protein is part of the morbilliviral cell entry machinery. Here, we present the cryo-electron microscopy (cryo-EM) structure and supramolecular organization of the tetrameric CDV H-protein ectodomain. The structure reveals that the morbilliviral H-protein is composed of three main domains: stalk, neck, and heads. The most unexpected feature was the inherent asymmetric architecture of the CDV H-tetramer being shaped by the neck, which folds into an almost 90° bent conformation with respect to the stalk. Consequently, two non-contacting receptor-binding H-head dimers, which are also tilted toward each other, are located on one side of an intertwined four helical bundle stalk domain. Positioning of the four protomer polypeptide chains within the neck domain is guided by a glycine residue (G158), which forms a hinge point exclusively in two protomer polypeptide chains. Molecular dynamics simulations validated the stability of the asymmetric structure under near physiological conditions and molecular docking showed that two receptor-binding sites are fully accessible. Thus, this spatial organization of the CDV H-tetramer would allow for concomitant protein interactions with the stalk and head domains without steric clashes. In summary, the structure of the CDV H-protein ectodomain provides new insights into the morbilliviral cell entry system and offers a blueprint for next-generation structure-based antiviral drug discovery.
History
DepositionApr 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin glycoprotein
B: Hemagglutinin glycoprotein
C: Hemagglutinin glycoprotein
D: Hemagglutinin glycoprotein


Theoretical massNumber of molelcules
Total (without water)273,2444
Polymers273,2444
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area12360 Å2
ΔGint-126 kcal/mol
Surface area81510 Å2

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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.) Canine morbillivirus / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9QPQ8

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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

ComponentName: Canine morbillivirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.272 MDa / Experimental value: NO
Source (natural)Organism: Canine morbillivirus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-Amino-2-hydroxymethyl-propane-1,3-diolTRIS1
2100 mMsodium chlorideNaCl1
30.1 %n-Octyl-beta-d-glucosideOG1
SpecimenConc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 3.5 sec Blot Force: -6 Drain Time: 0 Wait Time: 0

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 8000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 26835
Details: Two Datasets from two different grids were recorded: 13,760 and 13,075 movies

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Processing

SoftwareName: PHENIX / Version: 1.20_4459: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2SerialEMimage acquisition
4CTFFIND4.1.14CTF correction
7UCSF Chimera1.14model fitting
9RELION3.1.1initial Euler assignment
10cryoSPARC3.2.0final Euler assignment
11cryoSPARC3.2.0classification
12cryoSPARC3.2.03D reconstruction
13PHENIX1.20_4459model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 6471114
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 663258 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415126
ELECTRON MICROSCOPYf_angle_d0.60120618
ELECTRON MICROSCOPYf_dihedral_angle_d4.1852046
ELECTRON MICROSCOPYf_chiral_restr0.0462351
ELECTRON MICROSCOPYf_plane_restr0.0042638

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