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- PDB-9eac: Seneca valley virus Empty rotated particle at acidic condition (E... -

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Basic information

Entry
Database: PDB / ID: 9eac
TitleSeneca valley virus Empty rotated particle at acidic condition (ER-particle[C])
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 / entry receptor-mediated virion attachment to host cell / cysteine-type deubiquitinase activity / 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: 4.27 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: Rosheny Kumaran / Nadishka Jayawardena / Kuan-Lin Chen / Alice-Roza Eruera / James Hodgkinson-Bean / Laura N Burga / Matthias Wolf / Mihnea Bostina /
Abstract: Picornavirus cell entry requires a series of capsid protein conformational changes leading to genome uncoating. For enteroviruses, receptor binding triggers the transition from a full (F) capsid to ...Picornavirus cell entry requires a series of capsid protein conformational changes leading to genome uncoating. For enteroviruses, receptor binding triggers the transition from a full (F) capsid to an altered (A) particle before releasing its genome and finally converting it into an empty (E) particle. In contrast, non-enteroviruses, such as Aphthovirus, Cardiovirus, or Seneca Valley virus, release their genomes by dissociating the capsid into pentamers. While the existence of a transient A-particle for non-enteroviruses was previously speculated, it has never been directly observed using structural methods. Seneca Valley virus (SVV) is an oncolytic picornavirus that selectively targets cancer cells by recognizing Tumor endothelial marker 8 (TEM8) as the host receptor. SVV disassembles into pentamers at acidic pH, suggesting that the acidic environment of the endosome could cause capsid disassembly. We used cryo-electron microscopy to investigate SVV under acidic conditions and in complex with TEM8 at physiological pH, identifying multiple uncoating intermediates. These include an altered-particle, an empty-rotated particle (E), and a series of open particles expelling the coiled genome. The A-particle is expanded, displays reduced interactions between capsid proteins, a reorganized genome, and has a poorly resolved VP1 N-terminus, VP2 N-terminus, and VP4. The E particle has rotated pentamers, reduced contacts within the particle, lacks the genome, VP1 and VP2 N-termini, and VP4. Our work provides an understanding of transient SVV structural states and supports the existence of an intermediate SVV A-particle. These findings could help optimize SVV for oncolytic therapy.IMPORTANCESeneca Valley virus (SVV) is a non-enterovirus picornavirus with specific tumor tropism mediated by the receptor Tumor endothelial marker 8, also known as Anthrax toxin receptor 1. Using cryo-electron microscopy, it was possible to identify multiple structural states of SVV. We demonstrate that SVV capsids transition from full particles to altered (A) particles and then to empty-rotated (E) particles, with receptor binding and acidic pH driving these conformational changes, respectively. This study also identifies open particles with expelled genomes. Comparisons between A- and E-particles reveal that peptide segments of VP1, VP2, and VP4 could potentially play a role in genome delivery. Future work can explore the formation of these structural states .
History
DepositionNov 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _em_admin.last_update
Revision 1.2Oct 1, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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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)76,6704
Polymers76,6303
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)4,600,192240
Polymers4,597,787180
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: 25751.248 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: 24524.602 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: 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
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
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242 / 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_d0.0025024
ELECTRON MICROSCOPYf_angle_d0.4846895
ELECTRON MICROSCOPYf_dihedral_angle_d4.136728
ELECTRON MICROSCOPYf_chiral_restr0.042720
ELECTRON MICROSCOPYf_plane_restr0.004934

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