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- EMDB-54622: Echovirus 18 in situ, virion, I4 -

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Basic information

Entry
Database: EMDB / ID: EMD-54622
TitleEchovirus 18 in situ, virion, I4
Map data
Sample
  • Virus: Echovirus E18
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Echovirus 18 viral protein 2
    • Protein or peptide: Echovirus 18 viral protein 3
    • Protein or peptide: Echovirus 18 viral protein 4
KeywordsVirus / in situ structure
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 / ribonucleoside triphosphate phosphatase activity / 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 / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / 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 / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding
Similarity search - Function
Picornavirus coat protein VP4 superfamily / 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 VP4 superfamily / 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 speciesEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsMukhamedova L / Plevka P / Trebichalska Z / Novacek J
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Particles of echovirus 18 open to release their genomes in vivo.
Authors: Liya Mukhamedova / David Buchta / Zuzana Trebichalská / Yevgen Levdansky / Jana Moravcová / David Potěšil / Zbyněk Zdráhal / Dominik Hrebík / Lucie Nepovímová / Torleif Tollefsrud ...Authors: Liya Mukhamedova / David Buchta / Zuzana Trebichalská / Yevgen Levdansky / Jana Moravcová / David Potěšil / Zbyněk Zdráhal / Dominik Hrebík / Lucie Nepovímová / Torleif Tollefsrud Gjølberg / Jan Terje Andersen / Jiří Nováček / Tibor Füzik / Pavel Plevka /
Abstract: Enteroviruses cause a broad spectrum of human diseases, ranging from mild respiratory or gastrointestinal infections to severe neurological disorders such as aseptic meningitis and encephalitis. ...Enteroviruses cause a broad spectrum of human diseases, ranging from mild respiratory or gastrointestinal infections to severe neurological disorders such as aseptic meningitis and encephalitis. Enterovirus cell entry involves receptor-mediated endocytosis followed by destabilizing rearrangements of the virus capsid that enable genome release. However, the mechanism of enterovirus genome release has not been visualized in infected cells. Here, we used cryoelectron tomography and microscopy to image echovirus 18 (E18) entry into host cells and its interaction with the neonatal Fc receptor (FcRn). 30 min postinfection, endosomes and cytoplasm contained empty capsids missing one or several pentamers of capsid proteins, providing evidence that in vivo E18 releases its genome through capsid opening. In vitro, FcRn binding induced the expulsion of pocket factors from hydrophobic pockets in VP1, priming the virus for uncoating. The cryoelectron microscopy reconstruction of genome-containing particles of E18 inside infected cells did not reveal pocket factors, indicating that receptor binding triggers the same priming process during infection. We did not detect activated particles in infected cells, suggesting that these intermediates are short-lived and rapidly release their genomes in vivo. Our results identify capsid opening as the in vivo mechanism of echovirus 18 genome release, providing structural evidence for a process previously only inferred from in vitro experiments.
History
DepositionJul 30, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54622.png

Downloads & links

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Map

FileDownload / File: emd_54622.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å		2.08 Å/pix.
x 256 pix.
= 532.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 2.08047 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-6.475598 - 11.602575999999999
Average (Standard dev.)-0.000000001362618 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 532.60034 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54622_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Half map: MapB

Fileemd_54622_half_map_1.map
AnnotationMapB
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: MapA

Fileemd_54622_half_map_2.map
AnnotationMapA
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Histogram (log scale)

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Sample components

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Entire : Echovirus E18

EntireName: Echovirus E18
Components
  • Virus: Echovirus E18
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Echovirus 18 viral protein 2
    • Protein or peptide: Echovirus 18 viral protein 3
    • Protein or peptide: Echovirus 18 viral protein 4

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.9 MDa
Virus shellShell ID: 1 / Diameter: 330.0 Å

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 32.564445 KDa
SequenceString: GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT ...String:
GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT EGNAPPRISI PFISVGNAYS SFYDGWSHFT QDGTYGYTTL NAMGKLYIRH VNRSSPHQIT STIRVYFKPK HI KAWVPRP PRLCPYINKR DVNFVVTEIT DSRTSITDTP HPEHSVLATH

UniProtKB: Genome polyprotein

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Macromolecule #2: Echovirus 18 viral protein 2

MacromoleculeName: Echovirus 18 viral protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 28.802328 KDa
SequenceString: SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA ...String:
SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA VCNAGMGVGV GNLTIFPHQW INLRTNNSAT IVIPYINSVP MDNMFRHYNF TLMIIPFAPL NFTDGATAYV PI TVTIAPM YAEYNGLRLA STQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Echovirus 18 viral protein 3

MacromoleculeName: Echovirus 18 viral protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 26.143783 KDa
SequenceString: GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC ...String:
GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC VPWISQSHYR MVQQDPYTSA GYITCWYQTN IVVPPGAPTS CDVLCFASAC NDFSVRLLRD TPFMAQPGKL Q

UniProtKB: Genome polyprotein

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Macromolecule #4: Echovirus 18 viral protein 4

MacromoleculeName: Echovirus 18 viral protein 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 7.475322 KDa
SequenceString:
MGAQVSTQKT GAHETSLSAK GNSIIHYTNI NFYKDAASSA SNRQDIQQDP GKFTDPVKDL MIKTLPALN

UniProtKB: Genome polyprotein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1290 / Average exposure time: 8.0 sec. / Average electron dose: 34.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 42000
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hbk

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1337
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6hbk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9s63:
Echovirus 18 in situ, virion, I4

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