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- EMDB-56033: CryoEM structure of coxsackievirus B1 virus-like particle with VP... -

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Basic information

Entry
Database: EMDB / ID: EMD-56033
TitleCryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion
Map dataPrimary, unsharpened and unmasked 3DEM map obtained from SPA of CVB1 VLPs with the deletion of VP4 proteins. The map is shown at the 2.5 sigma contour level.
Sample
  • Virus: Coxsackievirus B1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
KeywordsCVB1 / VLP / vaccine candidate / enterovirus / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / : / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A ...Picornavirus coat protein VP4 superfamily / : / Picornavirus coat protein / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / 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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / 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 speciesCoxsackievirus B1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsLevanova AL / Guryanov S / Ahmad KLL / Butcher SJ
Funding support Finland, 3 items
OrganizationGrant numberCountry
Jane and Aatos Erkko Foundation240002 Finland
Sigrid Juselius Foundation95-7202-38 Finland
Sigrid Juselius Foundation121-8570-56 Finland
CitationJournal: J Biomed Sci / Year: 2026
Title: Coxsackie B1 virus-like particle that lacks VP4 protein demonstrates improved vaccine scalability, stability and immunogenicity.
Authors: Saana Soppela / Henna-Maarit Kyröläinen / Alesia Levanova / Magloire Pandoua Nekoua / Martín González-Rodríguez / Heini Lehto / Kiran L L Ahmad / Sergey Guryanov / Vesa P Hytönen / ...Authors: Saana Soppela / Henna-Maarit Kyröläinen / Alesia Levanova / Magloire Pandoua Nekoua / Martín González-Rodríguez / Heini Lehto / Kiran L L Ahmad / Sergey Guryanov / Vesa P Hytönen / Olli H Laitinen / Ilkka S Junttila / Didier Hober / Sarah J Butcher / Minna M Hankaniemi /
Abstract: BACKGROUND: Enteroviruses, including coxsackievirus B1 (CVB1), cause severe diseases such as myocarditis and meningitis, but vaccines are lacking for most enteroviruses. Conserved and immunodominant ...BACKGROUND: Enteroviruses, including coxsackievirus B1 (CVB1), cause severe diseases such as myocarditis and meningitis, but vaccines are lacking for most enteroviruses. Conserved and immunodominant epitopes, such as VP4 region and VP1 N-terminus may limit vaccine efficacy by inducing non-neutralizing antibody responses. Virus-like particles (VLPs) mimic native viruses without genetic material and can be engineered to exclude epitopes. To address these challenges, we developed a CVB1-VLP lacking VP4.
METHODS: Sequence conservation of CVB VP4 protein and the VP1 N-terminal PALXA region was assessed, and BALB/c mice were sequentially immunized with different formalin inactivated CVB vaccines. ...METHODS: Sequence conservation of CVB VP4 protein and the VP1 N-terminal PALXA region was assessed, and BALB/c mice were sequentially immunized with different formalin inactivated CVB vaccines. VLPΔVP4 was produced using baculovirus-insect cell expression system, was purified, and characterized by SDS-PAGE, transmission electron microscopy, dynamic light scattering, cryogenic electron microscopy, three-dimensional image reconstruction and atomic modelling. VLPΔVP4 stability was monitored over five years at 8 °C. Comprehensive preclinical experiments were conducted in mice with VLPΔVP4, VLPΔpalxa and inactivated CVB1. Vaccine immunogenicity was evaluated by neutralization assay, ELISA, ELISpot, and in vitro infection assays.
RESULTS: VP4- and PALXA-regions were conserved among CVB serotypes and sequential mouse vaccinations confirmed the induction of antibodies against these regions, that should be avoided in vaccination. ...RESULTS: VP4- and PALXA-regions were conserved among CVB serotypes and sequential mouse vaccinations confirmed the induction of antibodies against these regions, that should be avoided in vaccination. VLPΔVP4 exhibited > 95% purity, expected morphology (~ 30 nm), exceptional stability at 8 °C for five years, and the atomic modelling to 2.7 Å resolution showed that the particles were entirely in expanded form. Excluding VP4 from VLP improved production yield 3.5-fold, enhancing scalability of production. Immunological assays demonstrated that VLPΔVP4 induced slightly Th2-skewed response, but including adjuvant system 04 (AS04) in the vaccine induced balanced humoral and cellular immune response in mice. Sera from all vaccine groups modulated CVB1 infection, but IFN-α induction was lowest in VLP groups, suggesting reduced risk for antibody dependent enhancement of infection. VLPΔVP4 elicited significantly higher IFN-γ responses compared to other vaccines, indicating robust cellular immune response. Antibody responses were comparable across adjuvanted groups, but inclusion of VP4 in the vaccine correlated with weaker systemic T-cell responses.
CONCLUSIONS: VLPΔVP4 represents a promising next-generation CVB vaccine candidate with broad applicability against enteroviruses. Removal of VP4 may mitigate the risk for non-beneficial immune ...CONCLUSIONS: VLPΔVP4 represents a promising next-generation CVB vaccine candidate with broad applicability against enteroviruses. Removal of VP4 may mitigate the risk for non-beneficial immune imprinting while enabling high purity, long-term stability, and improved manufacturing efficiency.
History
DepositionDec 10, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56033.png

Downloads & links

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Map

FileDownload / File: emd_56033.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary, unsharpened and unmasked 3DEM map obtained from SPA of CVB1 VLPs with the deletion of VP4 proteins. The map is shown at the 2.5 sigma contour level.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 450 pix.
= 410.85 Å		0.91 Å/pix.
x 450 pix.
= 410.85 Å		0.91 Å/pix.
x 450 pix.
= 410.85 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.913 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035431
Minimum - Maximum-0.034886826 - 0.14073572
Average (Standard dev.)0.0036063632 (±0.012725908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 410.85 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A of the primary map shown at the 2.5 sigma contour level.

Fileemd_56033_half_map_1.map
AnnotationHalf-map A of the primary map shown at the 2.5 sigma contour level.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the primary map shown at the 2.5 sigma contour level.

Fileemd_56033_half_map_2.map
AnnotationHalf-map B of the primary map shown at the 2.5 sigma contour level.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Coxsackievirus B1

EntireName: Coxsackievirus B1
Components
  • Virus: Coxsackievirus B1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Coxsackievirus B1

SupramoleculeName: Coxsackievirus B1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12071 / Sci species name: Coxsackievirus B1 / Virus type: VIRUS-LIKE PARTICLE / 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: Coxsackievirus B1 / Strain: wild type strain 10796
Molecular weightTheoretical: 31.197047 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GPVEESVERA MVRVADTVSS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR AACVYYATYT NNSEKGYAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA TSVDAPVQTH QIMYVPPGGP VPTKVTDYAW Q TSTNPSVF ...String:
GPVEESVERA MVRVADTVSS RPTNSESIPA LTAAETGHTS QVVPSDTMQT RHVKNYHSRS ESSIENFLCR AACVYYATYT NNSEKGYAE WVINTRQVAQ LRRKLELFTY LRFDLELTFV ITSAQQPSTA TSVDAPVQTH QIMYVPPGGP VPTKVTDYAW Q TSTNPSVF WTEGNAPPRM SIPFISIGNA YSCFYDGWTQ FSRNGVYGIN TLNNMGTLYM RHVNEAGQGP IKSTVRIYFK PK HVKAWVP RPPRLCQYEK QKNVNFTPTG VTTTRVGITT T

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1 / Strain: wild type strain 10796
Molecular weightTheoretical: 29.137799 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SPSAEECGFS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFAELSGG DTARMFTDTQ I GETNSKKV ...String:
SPSAEECGFS DRVRSITLGN STITTQECAN VVVGYGVWPE YLKDNEATAE DQPTQPDVAT CRFYTLESVQ WMKNSAGWWW KLPDALSQM GLFGQNMQYH YLGRTGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCSNLNN TPEFAELSGG DTARMFTDTQ I GETNSKKV QTAVWNAGMG VGVGNLTIYP HQWINLRTNN SATIVMPYIN SVPMDNMFRH NNLTLMIIPF VPLNYSEGSS PY VPITVTI APMCAEYNGL RLASSQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Coxsackievirus B1 / Strain: wild type strain 10796
Molecular weightTheoretical: 26.268756 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTEA NVNSLKAYQI PVQSNSDNGK QVFGFPLQP GANGVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTEA NVNSLKAYQI PVQSNSDNGK QVFGFPLQP GANGVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVEDEYTAAG YITCWYQTNI VVPADVQSSC DILCFVSACN DFSVRMLKDT PFIRQDTFYQ

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

BufferpH: 7.4 / Details: 40 mM Tris-HCL, 10 mM MgCl2, 40 mM NaCL
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 298 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 150000
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9t0q
PDB Unreleased entry

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 53853
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9t0q
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9tkm:
CryoEM structure of coxsackievirus B1 virus-like particle with VP4 deletion

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