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- PDB-8cxp: Characterisation of a Seneca Valley Virus Thermostable Mutant -

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Basic information

Entry
Database: PDB / ID: 8cxp
TitleCharacterisation of a Seneca Valley Virus Thermostable Mutant
Components
  • Capsid protein VP1
  • Capsid protein VP3
  • VP2
  • VP4
KeywordsVIRUS / Picornavirus / SVV / Seneca Valley Virus / Oncolytic virus
Function / homology
Function and homology information


host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription ...host cell nucleolus / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus ...Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesSenecavirus A
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsJayawardena, N. / Bostina, M. / Strauss, M.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Not funded New Zealand
CitationJournal: 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
DepositionMay 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP3
C: VP2
D: VP4


Theoretical massNumber of molelcules
Total (without water)94,6974
Polymers94,6974
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP3
C: VP2
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,681,811240
Polymers5,681,811240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP3
C: VP2
D: VP4
x 5


  • icosahedral pentamer
  • 473 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)473,48420
Polymers473,48420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP3
C: VP2
D: VP4
x 6


  • icosahedral 23 hexamer
  • 568 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)568,18124
Polymers568,18124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein VP1


Mass: 29092.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YC68
#2: Protein Capsid protein VP3


Mass: 26492.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YC94
#3: Protein VP2


Mass: 31718.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A1U9IRU2
#4: Protein VP4


Mass: 7393.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Senecavirus A / References: UniProt: A0A649YCC5

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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: Senecavirus A / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Senecavirus A
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Sus scrofa
Virus shellName: Capsid / Diameter: 150 nm
Buffer solutionpH: 7.3
SpecimenConc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: OTHER
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 68 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1particle selection
2SerialEM3.9image acquisition
4RELION3.1CTF correction
7ISOLDEmodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 211958
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113052 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT
Atomic model buildingPDB-ID: 3CJI

3cji


Accession code: 3CJI / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056440
ELECTRON MICROSCOPYf_angle_d0.9268816
ELECTRON MICROSCOPYf_dihedral_angle_d9.7693801
ELECTRON MICROSCOPYf_chiral_restr0.055972
ELECTRON MICROSCOPYf_plane_restr0.0081149

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