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- EMDB-45179: Cryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus... -

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Basic information

Entry
Database: EMDB / ID: EMD-45179
TitleCryo-EM Structure of EV-D68 Vaccine Candidate - A2 Subclade Virus-like Particle
Map data
Sample
  • Virus: Enterovirus
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3
KeywordsEV-D68 / A2 subclade / VLP / 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / viral capsid / nucleoside-triphosphate phosphatase / channel 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 / ribonucleoside triphosphate phosphatase activity / host cell cytoplasmic vesicle membrane / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / symbiont-mediated suppression of host gene expression / 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 / membrane
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 (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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman enterovirus D68 / Enterovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.43 Å
AuthorsCheng J / Krug PW / Lei H / Moss DL / Huang R / Lang ZC / Morton AJ / Shen C / Pierson TC / Zhou T ...Cheng J / Krug PW / Lei H / Moss DL / Huang R / Lang ZC / Morton AJ / Shen C / Pierson TC / Zhou T / Ruckwardt TJ / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights from vaccine candidates for EV-D68.
Authors: Jiaxuan Cheng / Peter W Krug / Haotian Lei / Daniel L Moss / Zabrina C Lang / Abraham J Morton / Chen-Hsiang Shen / Sergei Pletnev / Rick K Huang / Theodore C Pierson / Tongqing Zhou / Tracy ...Authors: Jiaxuan Cheng / Peter W Krug / Haotian Lei / Daniel L Moss / Zabrina C Lang / Abraham J Morton / Chen-Hsiang Shen / Sergei Pletnev / Rick K Huang / Theodore C Pierson / Tongqing Zhou / Tracy J Ruckwardt / Peter D Kwong /
Abstract: Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we ...Enterovirus D68 (EV-D68), a member of the Picornaviridae family, causes respiratory illness and can lead to acute flaccid myelitis in children. No specific treatment or vaccine is available. Here, we determine cryo-EM structures of EV-D68 virus-like particles (VLPs), inactivated virus particles (InVPs), and altered virus particles (A-particles) from B3 and A2 subclades. The B3 VLP is a current vaccine candidate, which we show closely resembles its InVP counterpart, particularly at the 5-fold axis of symmetry, the target of potent neutralizing antibodies. Similar structural conservation was observed in the A2 subclade. Sequence variation between B3 and A2 mainly occurred in flexible loops displayed on the particle surface. A canyon-filling pocket factor was present in B3 InVP but absent in A2 InVP. A-particles were predominant in β-propiolactone-inactivated virus at longer but not shorter incubation. Overall, our findings highlight EV-D68 similarities and subclade-specific differences, offering structural insights that relate to vaccine development.
History
DepositionJun 3, 2024-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45179.png

Downloads & links

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Map

FileDownload / File: emd_45179.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å		0.83 Å/pix.
x 640 pix.
= 531.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-0.16044943 - 0.58988154
Average (Standard dev.)0.0075285463 (±0.033098802)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 531.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45179_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_45179_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Enterovirus

EntireName: Enterovirus
Components
  • Virus: Enterovirus
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3

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Supramolecule #1: Enterovirus

SupramoleculeName: Enterovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12059 / Sci species name: Enterovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 33.014531 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IESIIKTATD TVKSEINAEL GVVPSLNAVE TGASSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKNHT SSEARTDKN FYKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVGS NNSTYMGLPD LTLQAMFVPT GALTPEKQDS F HWQSGSNA ...String:
IESIIKTATD TVKSEINAEL GVVPSLNAVE TGASSNTEPE EAIQTRTVIN QHGVSETLVE NFLSRAALVS KRSFEYKNHT SSEARTDKN FYKWTINTKS FVQLRRKLEL FTYLRFDAEI TILTTVAVGS NNSTYMGLPD LTLQAMFVPT GALTPEKQDS F HWQSGSNA SVFFKVSDPP ARMTIPFMCI NSAYSVFYDG FAGFEKNGLY GINPADTIGN LCVRIVNEHQ PIGFTVTVRV YM KPKHIKA WAPRPPRTLP YMSIANANYK GKERAPNALN AIIGNRESVK TMPHDIRLV

UniProtKB: Genome polyprotein

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Macromolecule #2: VP0

MacromoleculeName: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 35.074316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLKS PSAEACGYSD RVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETESTGWWW KLPDALNNIG M FGQNVQHH ...String:
MGAQVTRQQT GTHENANIAT NGSHITYNQI NFYKDSYAAS ASKQDFSQDP SKFTEPVVEG LKAGAPVLKS PSAEACGYSD RVLQLKLGN SAIVTQEAAN YCCAYGEWPN YLPDHEAVAI DKPTQPETAT DRFYTLKSVK WETESTGWWW KLPDALNNIG M FGQNVQHH YLYRSGFLIH VQCNATKFHQ GALLVVAIPE HQRGAHNTTT SPGFDDIMKG EEGGTFNHPY VLDDGTSLAC AT IFPHQWI NLRTNNSATI VLPWMNAAPM DFPLRHNQWT LAIIPVVPLG TRTVSSMVPI TVSIAPMCCE FNGLRHAITQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human enterovirus D68
Molecular weightTheoretical: 27.282035 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVIQVE SMMEINNTEN AVGMQRLKVD ISVLTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLVIP ...String:
GVPTYLLPGS GQFLTTDDHS SAPVLPCFNP TPEMHIPGQV RNMLEVIQVE SMMEINNTEN AVGMQRLKVD ISVLTDVDQL LFNIPLDIQ LDGPLRNTLV GNISRYYTHW SGSLEMTFMF CGSFMATGKL ILCYTPPGGS CPTTRETAML GTHIVWDFGL Q SSVTLVIP WISGSHYRMF NNDAKSTNAN VGYVTCFMQT NLIVPSESSN TCSLIGFVAA KDDFSLRLMR DSPDIGQLEH LH EAEAAYQ

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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / 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:

6wdt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 37000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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