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Yorodumi- PDB-8r5x: Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroup... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r5x | ||||||
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Title | Structure of coxsackievirus B5 capsid (mutant CVB5F.cas.genogroupB) - F particle | ||||||
Components | Coxsackievirus B5 (mutant CVB5F.cas.genogroupB) - VP1 | ||||||
Keywords | VIRUS / Enterovirus / coxsackievirus / thermostable / mutant | ||||||
Function / homology | PALMITIC ACID Function and homology information | ||||||
Biological species | Coxsackievirus B5 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
Authors | Kumar, K. / Antanasijevic, A. | ||||||
Funding support | 1items
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Citation | Journal: Environ Sci Technol / Year: 2024 Title: Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation. Authors: Shotaro Torii / Jérôme Gouttenoire / Kiruthika Kumar / Aleksandar Antanasijevic / Tamar Kohn / Abstract: The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions ...The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r5x.cif.gz | 213.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r5x.ent.gz | 141.4 KB | Display | PDB format |
PDBx/mmJSON format | 8r5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r5x_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8r5x_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8r5x_validation.xml.gz | 48.2 KB | Display | |
Data in CIF | 8r5x_validation.cif.gz | 69.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/8r5x ftp://data.pdbj.org/pub/pdb/validation_reports/r5/8r5x | HTTPS FTP |
-Related structure data
Related structure data | 18942MC 8r5yC 8r5zC 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: 93795.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxsackievirus B5 / Cell line (production host): BGMK / Production host: Homo sapiens (human) #2: Chemical | ChemComp-PLM / | Has ligand of interest | N | |
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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: Coxsackievirus B5 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||
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Source (natural) | Organism: Coxsackievirus B5 | |||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: BGMK | |||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | |||||||||||||||
Natural host | Organism: Homo sapiens | |||||||||||||||
Virus shell | Name: Capsid VP1-4 / Diameter: 300 nm | |||||||||||||||
Buffer solution | pH: 7.5 / Details: TBS | |||||||||||||||
Buffer component |
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Specimen | Conc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: Inactivated by formaldehyde. Purified using a combination of sucrose gradient and size-exclusion chromatography. | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K Details: 3ul of sample applied. Blotting time varied. Blotting force = 0. Total blots = 1. |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 150000 X / Nominal defocus max: 1000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 6653 |
-Processing
EM software |
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Image processing | Details: EER files were imported to cryoSPARC live and motion correction was performed with Patch. | |||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 161820 / Details: Template picker used | |||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | |||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193 / Algorithm: BACK PROJECTION / Details: Non-uniform refinement / Num. of class averages: 1 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL Details: Initial fitting was performed in Chimera and model refinement was performed in Coot and Rosetta. | |||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7C9Y Accession code: 7C9Y Details: Asymmetric unit used for fitting and interpretation Source name: PDB / Type: experimental model |