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- EMDB-47829: Seneca valley virus Empty rotated particle at acidic condition (E... -

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Basic information

Entry
Database: EMDB / ID: EMD-47829
TitleSeneca valley virus Empty rotated particle at acidic condition (ER-particle[C])
Map data
Sample
  • Virus: Seneca Valley virus USA/SSV-001
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP2
  • Ligand: CALCIUM ION
KeywordsSVV / Capsid / Physiological condition / Virus / 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
Methodsingle particle reconstruction / cryo EM / Resolution: 4.27 Å
AuthorsKumaran R / Bostina M
Funding support1 items
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 KL / Eruera AR / Hodgkinson-Bean J / Burga LN / Wolf M / Bostina M
History
DepositionNov 10, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47829.png

Downloads & links

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Map

FileDownload / File: emd_47829.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 330 pix.
= 462. Å		1.4 Å/pix.
x 330 pix.
= 462. Å		1.4 Å/pix.
x 330 pix.
= 462. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.726
Minimum - Maximum-0.8467902 - 2.1616817
Average (Standard dev.)0.034672707 (±0.22175744)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 462.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_47829_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47829_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_47829_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Seneca Valley virus USA/SSV-001

EntireName: Seneca Valley virus USA/SSV-001
Components
  • Virus: Seneca Valley virus USA/SSV-001
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP3
    • Protein or peptide: Capsid protein VP2
  • Ligand: CALCIUM ION

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Supramolecule #1: Seneca Valley virus USA/SSV-001

SupramoleculeName: Seneca Valley virus USA/SSV-001 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / NCBI-ID: 686944 / Sci species name: Seneca Valley virus USA/SSV-001 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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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: Seneca Valley virus USA/SSV-001
Molecular weightTheoretical: 25.751248 KDa
SequenceString: NHTNVKFLFD RSRLLNVIKV LEKDAVFPRP FPTQEGAQQD DGYFCLLTPR PTVASRPATR FGLYANPSGS GVLANTSLDF NFYSLACFT YFRSDLEVTV VSLEPDLEFA VGWFPSGSEY QASSFVYDQL HVPFHFTGRT PRAFASKGGK VSFVLPWNSV S SVLPVRWG ...String:
NHTNVKFLFD RSRLLNVIKV LEKDAVFPRP FPTQEGAQQD DGYFCLLTPR PTVASRPATR FGLYANPSGS GVLANTSLDF NFYSLACFT YFRSDLEVTV VSLEPDLEFA VGWFPSGSEY QASSFVYDQL HVPFHFTGRT PRAFASKGGK VSFVLPWNSV S SVLPVRWG GASKLSSATR GLPAHADWGT IYAFVPRPNE KKSTAVKHVA VYIRYKNARA WCPSMLPFRS YK

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: Seneca Valley virus USA/SSV-001
Molecular weightTheoretical: 26.353938 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

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Seneca Valley virus USA/SSV-001
Molecular weightTheoretical: 24.524602 KDa
SequenceString: WYTGRLNSWT KAVKTFSFQA VPLPGAFLSR QGGLNGGAFT ATLHRHFLMK CGWQVQVQCN LTQFHQGALL VAMVPETTLD VKPDGKAKS LQELNEEQWV EMSDDYRTGK NMPFQSLGTY YRPPNWTWGP NFINPYQVTV FPHQILNART STSVDINVPY I GETPTQSS ...String:
WYTGRLNSWT KAVKTFSFQA VPLPGAFLSR QGGLNGGAFT ATLHRHFLMK CGWQVQVQCN LTQFHQGALL VAMVPETTLD VKPDGKAKS LQELNEEQWV EMSDDYRTGK NMPFQSLGTY YRPPNWTWGP NFINPYQVTV FPHQILNART STSVDINVPY I GETPTQSS ETQNSWTLLV MVLVPLDYKE GATTDPEITF SVRPTSPYFN GLRNRYTAG

UniProtKB: Genome polyprotein

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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

Concentration0.25 mg/mL
BufferpH: 5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 310.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSVV 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.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3cji

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 242
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

3cji

chain_id: A, residue_range: 1-258, source_name: PDB, initial_model_type: experimental model

3cji

chain_id: B, residue_range: 1-238, source_name: PDB, initial_model_type: experimental model

3cji

chain_id: C, residue_range: 13-279, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9eac:
Seneca valley virus Empty rotated particle at acidic condition (ER-particle[C])

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