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- EMDB-27066: Characterisation of a Seneca Valley Virus Thermostable Mutant -

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Basic information

Entry
Database: EMDB / ID: EMD-27066
TitleCharacterisation of a Seneca Valley Virus Thermostable Mutant
Map dataSeneca Valley Virus Thermostable Mutant
Sample
  • Virus: Senecavirus A
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4
KeywordsVirus / 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 / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 2.47 Å
AuthorsJayawardena N / Bostina M / Strauss M
Funding support New Zealand, 1 items
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, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27066.png

Downloads & links

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Map

FileDownload / File: emd_27066.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSeneca Valley Virus Thermostable Mutant
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.7294473 - 1.1389424
Average (Standard dev.)-0.0093693705 (±0.066666804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 533.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27066_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27066_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Senecavirus A

EntireName: Senecavirus A
Components
  • Virus: Senecavirus A
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: VP2
    • Protein or peptide: VP4

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Supramolecule #1: Senecavirus A

SupramoleculeName: Senecavirus A / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 390157 / Sci species name: Senecavirus A / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Sus scrofa (pig)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 150.0 Å

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 29.092826 KDa
SequenceString: STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP ...String:
STDNAETGVI EAGNTDTDFS GELAAPGSNH TNVKFLFDRS RLLNVIKVLE KDAVFPRPFP TQEGAQQDDG YFCLLTPRPT VASRPATRF GLYANPSGSG VLANTSLDFN FYSLACFTYF RSDLEVTVVS LEPDLEFAVG WFPSGSEYQA SSFVYDQLHV P FHFTGRTP RAFASKGGKV SFVLPWNSVS SVLPVRWGGA SKLSSATRGL PAHADWGTIY AFVPRPNEKK STAVKHVAVY IR YKNARAW CPSMLPFRSY KQKMLM

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 26.492084 KDa
SequenceString: GPIPTAPREN SLMFLSTLPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFERVP EPVPASDTYV PYVAVPTQFD DRPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV ...String:
GPIPTAPREN SLMFLSTLPD DTVPAYGNVR TPPVNYLPGE ITDLLQLARI PTLMAFERVP EPVPASDTYV PYVAVPTQFD DRPLISFPI TLSDPVYQNT LVGAISSNFA NYRGCIQITL TFCGPMMARG KFLLSYSPPN GTQPQTLSEA MQCTYSIWDI G LNSSWTFV VPYISPSDYR ETRAITNSVY SADGWFSLHK LTKITLPPDC PQSPCILFFA SAGEDYTLRL PVDCNPSYVF H

UniProtKB: Genome polyprotein

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 31.718062 KDa
SequenceString: DHNTEEMENS ADRVTTQTAG NTAINTQSSL GVLCAYVEDP TKSDPPSSST DQPTTTFTAI DRWYTGRLNS WTKAVKTFSF QAVPLPGAF LSRQGGLNGG AFTATLHRHF LMKCGWQVQV QCNLTQFHQG ALLVAMVPET TLDVKPDGKA KSLQELNEEQ W VEMSDDYR ...String:
DHNTEEMENS ADRVTTQTAG NTAINTQSSL GVLCAYVEDP TKSDPPSSST DQPTTTFTAI DRWYTGRLNS WTKAVKTFSF QAVPLPGAF LSRQGGLNGG AFTATLHRHF LMKCGWQVQV QCNLTQFHQG ALLVAMVPET TLDVKPDGKA KSLQELNEEQ W VEMSDDYR TGKNMPFQSL GTYYRPPNWT WGPNFINPYQ VTVFPHQILN ARTSTSVDVN VPYIGETPTQ SSETQNSWTL LV MVLVPLD YKEGATTDPE ITFSVRPTSP YFNGLRNRYT AGTDEEQ

UniProtKB: Genome polyprotein

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Senecavirus A
Molecular weightTheoretical: 7.393875 KDa
SequenceString:
GNVQTTSKND FDSRGNNGNM TFNYYANTYQ NSVDFSTSSS ASGAGPGNSR GGLAGLLTNF SGILNPLGYL K

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.34 mg/mL
BufferpH: 7.3
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 211958
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3cji

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.47 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 113052
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

3cji


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: FLEXIBLE FIT
Output model

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

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