+Open data
-Basic information
Entry | Database: PDB / ID: 8cxp | ||||||
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Title | Characterisation of a Seneca Valley Virus Thermostable Mutant | ||||||
Components |
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Keywords | VIRUS / Picornavirus / SVV / Seneca Valley Virus / Oncolytic virus | ||||||
Function / homology | Function and homology information RNA-protein covalent cross-linking / : / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell ...RNA-protein covalent cross-linking / : / : / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / symbiont entry into host cell / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding Similarity search - Function | ||||||
Biological species | Senecavirus A | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å | ||||||
Authors | Jayawardena, N. / Bostina, M. / Strauss, M. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Virology / Year: 2022 Title: Characterisation of a Seneca Valley virus thermostable mutant. Authors: Nadishka Jayawardena / Cormac McCarthy / Ivy Wang / Shakeel Waqqar / Laura N Burga / Mike Strauss / Mihnea Bostina / Abstract: Seneca Valley virus (SVV) is a newly discovered picornavirus in the Senecavirus genus. SVV-001 strain has shown promise as an oncolytic virus against tumors with neuroendocrine features. There is a ...Seneca Valley virus (SVV) is a newly discovered picornavirus in the Senecavirus genus. SVV-001 strain has shown promise as an oncolytic virus against tumors with neuroendocrine features. There is a need to use a structure-based approach to develop virus-like particles capable to mimicking the architecture of naturally occurring empty capsids that can be used as vaccines or as carriers for targeted cancer treatment. However, these empty capsids are inherently less stable, and tedious to purify. This warrants investigation into factors which confer the SVV capsid stability and into combining this knowledge to recombinantly express stable SVV VLPs. In this study, we isolated a thermostable mutant of SVV by thermal selection assays and we characterized a single mutation located in a capsid protein. The cryo-EM map of this mutant showed conformational shifts that facilitated the formation of additional hydrogen bonds and aromatic interactions, which could serve as capsid stabilizing factors. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cxp.cif.gz | 151.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cxp.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8cxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cxp_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8cxp_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8cxp_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 8cxp_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/8cxp ftp://data.pdbj.org/pub/pdb/validation_reports/cx/8cxp | HTTPS FTP |
-Related structure data
Related structure data | 27066MC 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
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 29092.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YC68 |
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#2: Protein | Mass: 26492.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YC94 |
#3: Protein | Mass: 31718.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2 |
#4: Protein | Mass: 7393.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YCC5 |
-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: Senecavirus A / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Senecavirus A |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Sus scrofa |
Virus shell | Name: Capsid / Diameter: 150 nm |
Buffer solution | pH: 7.3 |
Specimen | Conc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-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: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 68 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / 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: 211958 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113052 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3CJI Accession code: 3CJI / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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