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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-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 / endocytosis involved in viral entry into host cell / 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 / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / : / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion 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 ...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 / 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. / 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: 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-
UpdateJul 31, 2024-
Current statusJul 31, 2024Processing 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: 0.97 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: 436.5 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: 25.013381 KDa
SequenceString: SRSESSIENF LCRSACVYYA TYTNNSKKGF AEWVINTRQV AQLRRKLELF TYLRFDLELT FVITSAQQPS TASSVDAPVQ THQIMYVPP GGPVPTKVKD YAWQTSTNPS VFWTEGNAPP RMSIPFISIG NAYSCFYDGW TQFSRNGVYG INTLNNMGTL Y MRHVNEAG ...String:
SRSESSIENF LCRSACVYYA TYTNNSKKGF AEWVINTRQV AQLRRKLELF TYLRFDLELT FVITSAQQPS TASSVDAPVQ THQIMYVPP GGPVPTKVKD YAWQTSTNPS VFWTEGNAPP RMSIPFISIG NAYSCFYDGW TQFSRNGVYG INTLNNMGTL Y MRHVNEAG QGPIKSTVRI YFKPKHVKAW VPRPPRLCQY EKQKNVNFSP IGVTTSRTDI IT

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: 27.71035 KDa
SequenceString: RVRSITLGNS TITTQECNNV VVGYGVWPEY LKDNEATAED QPTQPDVATC RFYTLESVQW MKNSAGWWWK LPDALSQMGL FGQNMQYHY LGRTGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSNLNNT PEFSELSGGD SARMFTDTQV GESNAKKVQT A VWNAGMGV ...String:
RVRSITLGNS TITTQECNNV VVGYGVWPEY LKDNEATAED QPTQPDVATC RFYTLESVQW MKNSAGWWWK LPDALSQMGL FGQNMQYHY LGRTGYTIHV QCNASKFHQG CLLVVCVPEA EMGCSNLNNT PEFSELSGGD SARMFTDTQV GESNAKKVQT A VWNAGMGV GVGNLTIFPH QWINLRTNNS ATLVMPYINS 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: 25.545963 KDa
SequenceString: GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV ...String:
GLPVMTTPGS TQFLTSDDFQ SPSAMPQFDV TPEMQIPGRV NNLMEIAEVD SVVPVNNTED NVSSLKAYQI PVQSNSDNGK QVFGFPLQP GANNVLNRTL LGEILNYYTH WSGSIKLTFM FCGSAMATGK FLLAYSPPGA GVPKNRKDAM LGTHVIWDVG L QSSCVLCV PWISQTHYRY VVEDEYTAAG YVTCWYQTNI 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

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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