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- EMDB-65634: Cryo-EM structure of Enterovirus-D68 MO strain virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-65634
TitleCryo-EM structure of Enterovirus-D68 MO strain virus-like particle
Map data
Sample
  • Complex: Virus-like particle of enterovirus D68 consisting of Viral protein 1, Viral protein 0, and Viral protein 3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
KeywordsEnterovirus-D68 / MO strain / viral structural proteins / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


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 ...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 / RNA helicase activity / symbiont-mediated suppression of host innate immune response / 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 / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
: / 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 / 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 speciesenterovirus D68
Methodsingle particle reconstruction / cryo EM / Resolution: 2.57 Å
AuthorsSenpuku K / Hirose M / Ito T / Kato T / Yshioka Y
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24K22020 Japan
Japan Science and TechnologyJPMJSP2138 Japan
CitationJournal: Mol Ther Nucleic Acids / Year: 2026
Title: Comparative immunogenic and structural analysis of virus-like particle and inactivated whole-virion vaccines against enterovirus D68.
Authors: Kota Senpuku / Yuta Kunishima / Mika Hirose / Tatsuya Karaki / Kotaro Taniguchi / Chikako Kataoka-Nakamura / Toshiro Hirai / Koubun Yasuda / Etsushi Kuroda / Takayuki Kato / Taiki Ito / Yasuo Yoshioka /
Abstract: Enterovirus D68 (EV-D68) primarily causes respiratory illnesses and has been implicated in acute flaccid myelitis. Although virus-like particle (VLP) and traditional inactivated whole-virion (IWV) ...Enterovirus D68 (EV-D68) primarily causes respiratory illnesses and has been implicated in acute flaccid myelitis. Although virus-like particle (VLP) and traditional inactivated whole-virion (IWV) vaccines have demonstrated efficacy in mice, their immunological differences remain undetermined. Here, we directly compared the immunogenic and structural properties of VLP and IWV vaccines derived from the same EV-D68 strain under identical conditions. Although VLP induced significantly lower levels of EV-D68-specific IgG than IWV, neutralizing antibody titers and protective effects against viral challenge were comparable between the two groups in mice. Passive transfer experiments in neonatal mice further confirmed protection against lethal infection for both vaccine groups. Notably, in contrast to the IWV vaccine, the VLP vaccine elicited antibodies that preferentially recognized a limited subset of epitopes. Cryo-electron microscopy analyses revealed that VLPs structurally resemble the native virus but display distinct features in regions corresponding to epitopes that show differential antibody reactivity between VLP and IWV vaccines. By integrating structural and immunological analyses, we established a mechanistic framework linking capsid architecture to vaccine-induced antibody specificity. These findings suggest that VLP is a promising EV-D68 vaccine antigen with distinct epitope recognition profiles driven by structural characteristics.
History
DepositionJul 31, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65634.png

Downloads & links

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Map

FileDownload / File: emd_65634.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 400 pix.
= 445.44 Å		1.11 Å/pix.
x 400 pix.
= 445.44 Å		1.11 Å/pix.
x 400 pix.
= 445.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.17
Minimum - Maximum-9.974762 - 15.0362425
Average (Standard dev.)0.0044190157 (±0.8259005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 444.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65634_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65634_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Virus-like particle of enterovirus D68 consisting of Viral protei...

EntireName: Virus-like particle of enterovirus D68 consisting of Viral protein 1, Viral protein 0, and Viral protein 3
Components
  • Complex: Virus-like particle of enterovirus D68 consisting of Viral protein 1, Viral protein 0, and Viral protein 3
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Virus-like particle of enterovirus D68 consisting of Viral protei...

SupramoleculeName: Virus-like particle of enterovirus D68 consisting of Viral protein 1, Viral protein 0, and Viral protein 3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 5.64 MDa

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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: enterovirus D68
Molecular weightTheoretical: 32.920309 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGATSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKDHT SSTARADKN FFKWTINTRS FVQLRRKLEL FTYLRFDAEI TILTTVAVNG SGNNTYVGLP DLTLQAMFVP TGALTPEKQD S FHWQSGSN ASVFFKISDP PARITIPFMC INSAYSVFYD GFAGFEKNGL YGINPADTIG NLCVRIVNEH QPVGFTVTVR VY MKPKHIK AWAPRPPRTL PYMSIANANY KGKERAPNAL SAIIGNRDSV KTMPHNIVNT

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: enterovirus D68
Molecular weightTheoretical: 35.017227 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLKS PSAEACGYSD RVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNIG M FGQNVQHH ...String:
MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLKS PSAEACGYSD RVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETGSTGWWW KLPDALNNIG M FGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTNT SPGFDDIMKG EEGGTFNHPY VLDDGTSLAC AT IFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTTSSMVPI TVSIAPMCCE FNGLRHAITQ

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: enterovirus D68
Molecular weightTheoretical: 27.112814 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPALPCFNP TPEMHIPGQV RNMLEVVQVE SMMEINNTES AVGMERLKVD ISALTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMAAGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLIIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSD TCSLIGFIAA KDDFSLRLMR DSPDIGQLDH LH AAEAAYQ

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

Concentration1.6 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
137.0 mMNaClsodium chloride
2.68 mMKClPotassium chloride
8.1 mMNa2HPO4Disodium hydrogen phosphate
1.47 mMKH2PO4Potassium dihydrogen phosphate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microsope was modified wit a CEOS Cs corrector.
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 819 / Average exposure time: 7.82 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.594 µm / Calibrated defocus min: 0.109 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.061 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 274941
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.57 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 58404
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. 4.4.1)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9w4i:
Cryo-EM structure of Enterovirus-D68 MO strain virus-like particle

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