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Yorodumi- PDB-7zny: Cryo-EM structure of the canine distemper virus tetrameric attach... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zny | ||||||
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Title | Cryo-EM structure of the canine distemper virus tetrameric attachment glycoprotein | ||||||
Components | Hemagglutinin glycoprotein | ||||||
Keywords | VIRAL 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 | ||||||
Biological species | Canine morbillivirus | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å | ||||||
Model details | tetramer, four heads, one neck, ectodomain, viral protein | ||||||
Authors | Kalbermatter, D. / Jeckelmann, J.-M. / Wyss, M. / Plattet, P. / Fotiadis, D. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7zny.cif.gz | 364.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7zny.ent.gz | 301.2 KB | Display | PDB format |
PDBx/mmJSON format | 7zny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zny_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7zny_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7zny_validation.xml.gz | 61.8 KB | Display | |
Data in CIF | 7zny_validation.cif.gz | 91.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/7zny ftp://data.pdbj.org/pub/pdb/validation_reports/zn/7zny | HTTPS FTP |
-Related structure data
Related structure data | 14842MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Canine morbillivirus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 0.272 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Canine morbillivirus | ||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293 | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 1.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: 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 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 20000 nm / Nominal defocus min: 8000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average 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 |
-Processing
Software | Name: PHENIX / Version: 1.20_4459: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 6471114 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 663258 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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