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- PDB-9ead: Seneca valley virus Empty rotated particle at physiological condi... -

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Basic information

Entry
Database: PDB / ID: 9ead
TitleSeneca valley virus Empty rotated particle at physiological condition (ER-particle[P])
Components
  • Capsid protein VP1
  • Capsid protein VP2
  • Capsid protein VP3
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: 6.41 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,9144
Polymers76,8743
Non-polymers401
Water00
1
A: Capsid protein VP1
B: Capsid protein VP3
C: Capsid protein VP2
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)4,614,848240
Polymers4,612,443180
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: 25838.326 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: 24681.793 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Seneca Valley virus USA/SSV-001 / References: UniProt: Q155Z9
#4: 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-#3 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Seneca Valley virus USA/SSV-001
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: SVV was incubated with TEM8 with a receptor ratio of 600 receptors per capsid. It was held at 37 degree Celsius for 90 minutes prior being vitrified for Cryo EM.
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
13cryoSPARC4.5.33D reconstruction
14ISOLDE1.8model refinement
15Coot0.9.8.8model refinement
16PHENIX1.21.2-5419model refinement
17UCSF ChimeraX1.8model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137 / 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
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0035602
ELECTRON MICROSCOPYf_angle_d0.6157667
ELECTRON MICROSCOPYf_dihedral_angle_d6.53751
ELECTRON MICROSCOPYf_chiral_restr0.043837
ELECTRON MICROSCOPYf_plane_restr0.007992

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