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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
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: Senpuku K / Kunishima Y / Hirose M / Karaki T / Taniguchi K / Kataoka-Nakamura C / Hirai T / Yasuda K / Kuroda E / Kato T / Ito T / Yoshioka Y
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

FileReleased
Voxel sizeX=Y=Z: 1.11 Å
Density
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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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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