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- PDB-9eaa: Seneca valley virus Altered particle at acidic condition (A-parti... -

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Basic information

Entry
Database: PDB / ID: 9eaa
TitleSeneca valley virus Altered particle at acidic condition (A-particle[C])
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
  • Capsid protein VP4
KeywordsVIRUS / SVV / Capsid / Physiological condition / Non-enterovirus / A-particle / Altered particle / genome release / capsid uncoating / Seneca Valley virus / Senecavirus / Oncolytic virus
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF7 activity / host cell nucleolus / adhesion receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / entry receptor-mediated virion attachment to host cell / RNA helicase activity / RNA helicase / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / symbiont entry into host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane
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
Biological speciesSeneca Valley virus USA/SSV-001
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsKumaran, R. / Bostina, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Virol. / Year: 2025
Title: Cryo-EM structure of the Seneca Valley virus A-particle and related structural states
Authors: Kumaran, R. / Jayawardena, N. / Chen, K.L. / Eruera, A.R. / Hodgkinson-Bean, J. / Burga, L.N. / Wolf, M. / Bostina, M.
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release

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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: Capsid protein VP2
D: Capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7235
Polymers90,6834
Non-polymers401
Water00
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
D: Capsid protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,443,366300
Polymers5,440,961240
Non-polymers2,40560
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Capsid protein VP1 / Alpha / P1D / Virion protein 1


Mass: 28459.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca Valley virus USA/SSV-001 / References: UniProt: Q155Z9
#2: Protein Capsid protein VP3 / Gamma / P1C / Virion protein 3


Mass: 26353.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca Valley virus USA/SSV-001 / References: UniProt: Q155Z9
#3: Protein Capsid protein VP2 / Beta / P1B / Virion protein 2


Mass: 29870.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca Valley virus USA/SSV-001 / References: UniProt: Q155Z9
#4: Protein Capsid protein VP4 / P1A / Rho / Virion protein 4


Mass: 5998.467 Da / Num. of mol.: 1 / Fragment: UNP residues 93-150 / Source method: isolated from a natural source / Source: (natural) Seneca Valley virus USA/SSV-001 / References: UniProt: Q155Z9
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: Seneca Valley virus USA/SSV-001 / Type: VIRUS / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Seneca Valley virus USA/SSV-001
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 5
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: SVV was incubated at pH 5 for 1 hour. Then, a ratio of 600 receptor particles per capsid was added to the incubated sample. The virus-receptor mixture was incubated at 37 degrees C for 90 ...Details: SVV was incubated at pH 5 for 1 hour. Then, a ratio of 600 receptor particles per capsid was added to the incubated sample. The virus-receptor mixture was incubated at 37 degrees C for 90 minutes. The sample was kept at 37 degrees C until the plunge freezing of cryo-EM grids.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 310.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: OTHER / Nominal defocus max: 1500 nm / Nominal defocus min: 400 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.5.3particle selection
4cryoSPARC4.5.3CTF correctionPatch CTF
7ISOLDE1.8model fitting
8UCSF ChimeraX1.8model fitting
10ISOLDE1.8model refinement
11Coot0.9.8.8model refinement
12PHENIX1.21.2-5419model refinement
13UCSF ChimeraX1.8model refinement
17cryoSPARC4.5.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 817 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Atomic model building

3D fitting-ID: 1 / Accession code: 3cji / Initial refinement model-ID: 1 / PDB-ID: 3cji

3cji

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-IDChain residue rangePdb chain residue range
1AA1-2581-258
2BB1-2381-238
3CC13-27913-279
4DD14-7214-72
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0046331
ELECTRON MICROSCOPYf_angle_d0.5018665
ELECTRON MICROSCOPYf_dihedral_angle_d4.473859
ELECTRON MICROSCOPYf_chiral_restr0.042958
ELECTRON MICROSCOPYf_plane_restr0.0051127

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