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- EMDB-50500: Expanded formalin inactivated CVB1 -

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Basic information

Entry
Database: EMDB / ID: EMD-50500
TitleExpanded formalin inactivated CVB1
Map dataDensity map of expanded formalin inactivated CVB1 resolved at 3 A.
Sample
  • Virus: Coxsackievirus B1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
Keywordscoxsackievirus B1 / vaccine / formalin / VIRUS
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesCoxsackievirus B1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 Å
AuthorsPlavec Z / Butcher SJ
Funding support Finland, 4 items
OrganizationGrant numberCountry
Sigrid Juselius Foundation95-7202-38 Finland
Sigrid Juselius Foundation121-8570-56 Finland
Jane and Aatos Erkko Foundation210034 Finland
Jane and Aatos Erkko Foundation240002 Finland
CitationJournal: Res Sq / Year: 2024
Title: Comparison of structure and immunogenicity of CVB1-VLP and inactivated CVB1 vaccine candidates.
Authors: Saana Soppela / Zlatka Plavec / Stina Gröhn / Minne Jartti / Sami Oikarinen / Mira Laajala / Varpu Marjomaki / Sarah J Butcher / Minna M Hankaniemi
Abstract: Coxsackievirus B1 (CVB1) is a common cause of acute and chronic myocarditis, dilated cardiomyopathy and aseptic meningitis. However, no CVB-vaccines are available for human use. In this study, we ...Coxsackievirus B1 (CVB1) is a common cause of acute and chronic myocarditis, dilated cardiomyopathy and aseptic meningitis. However, no CVB-vaccines are available for human use. In this study, we investigated the immunogenicity of virus-like particle (VLP) and inactivated whole-virus vaccines for CVB1 when administrated to mice via either subcutaneous or intranasal routes formulated with and without commercial and experimental adjuvants. Here, the potential of utilizing epigallocatechin-3-gallate (EGCG) as a mucosal adjuvant synergistically with its ability to inactivate the virus were investigated. EGCG had promising adjuvant properties for CVB1-VLP when administered via the parenteral route but limited efficacy via intranasal administration. However, intranasal administration of the formalin-inactivated virus induced high CVB1-specific humoral, cellular, and mucosal immune responses. Also, based on CVB1-specific IgG-antibody responses, we conclude that CVB1-VLP can be taken up by immune cells when administrated intranasally and further structural engineering for the VLP may increase the mucosal immunogenicity. The preparations contained mixtures of compact and expanded A particles with 85% expanded in the formalin-inactivated virus, but only 52% in the VLP observed by cryogenic electron microscopy. To correlate the structure to immunogenicity, we solved the structures of the CVB1-VLP and the formalin-inactivated CVB1 virus at resolutions ranging from 2.15 A to 4.1 A for the expanded and compact VLP and virus particles by image reconstruction. These structures can be used in designing mutations increasing the stability and immunogenicity of CVB1-VLP in the future. Overall, our results highlight the potential of using formalin inactivated CVB1 vaccine in mucosal immunization programs and provide important information for future development of VLP-based vaccines against all enteroviruses.
History
DepositionMay 31, 2024-
Header (metadata) releaseJul 31, 2024-
Map releaseJul 31, 2024-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50500.png

Downloads & links

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Map

FileDownload / File: emd_50500.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map of expanded formalin inactivated CVB1 resolved at 3 A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 Å		0.97 Å/pix.
x 450 pix.
= 436.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.951 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.3708134 - 1.2394035
Average (Standard dev.)0.028433345 (±0.10177558)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 427.94998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of expanded formalin inactivated CVB1.

Fileemd_50500_half_map_1.map
AnnotationHalf map of expanded formalin inactivated CVB1.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of expanded formalin inactivated CVB1.

Fileemd_50500_half_map_2.map
AnnotationHalf map of expanded formalin inactivated CVB1.
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
Details: Coxsackievirus B1 (CVB1-10796, isolated from Argentina)
NCBI-ID: 12071 / Sci species name: Coxsackievirus B1 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Virus shellShell ID: 1 / Name: capsid

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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
Molecular weightTheoretical: 24.943195 KDa
SequenceString: SRSESSIENF LCRAACVYYA TYTNNSEKGY AEWVINTRQV AQLRRKLELF TYLRFDLELT FVITSAQQPS TATSVDAPVQ THQIMYVPP GGPVPTKVTD YAWQTSTNPS VFWTEGNAPP RMSIPFISIG NAYSCFYDGW TQFSRNGVYG INTLNNMGTL Y MRHVNEAG ...String:
SRSESSIENF LCRAACVYYA TYTNNSEKGY AEWVINTRQV AQLRRKLELF TYLRFDLELT FVITSAQQPS TATSVDAPVQ THQIMYVPP GGPVPTKVTD YAWQTSTNPS VFWTEGNAPP RMSIPFISIG NAYSCFYDGW TQFSRNGVYG INTLNNMGTL Y MRHVNEAG QGPIKSTVRI YFKPKHVKAW VPRPPRLCQY EKQKNVNFTP TGVTTTRVGI TT

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
Molecular weightTheoretical: 27.725402 KDa
SequenceString: RVRSITLGNS TITTQECANV VVGYGVWPEY LKDNEATAED QPTQPDVATC RFYTLESVQW MKNSAGWWWK LPDALSQMGL FGQNMQYHY LGRTGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSNLNNT PEFAELSGGD TARMFTDTQI GETNSKKVQT A VWNAGMGV ...String:
RVRSITLGNS TITTQECANV VVGYGVWPEY LKDNEATAED QPTQPDVATC RFYTLESVQW MKNSAGWWWK LPDALSQMGL FGQNMQYHY LGRTGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSNLNNT PEFAELSGGD TARMFTDTQI GETNSKKVQT A VWNAGMGV GVGNLTIYPH QWINLRTNNS ATIVMPYINS VPMDNMFRHN NLTLMIIPFV PLNYSEGSSP YVPITVTIAP MC AEYNGLR LA

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
Molecular weightTheoretical: 25.485955 KDa
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 PFIR

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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / 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: 2.8000000000000003 µm / Nominal defocus min: 0.1 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1935
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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