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- PDB-9tf0: Structure of echovirus 18 in complex with neonatal Fc receptor -

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Basic information

Entry
Database: PDB / ID: 9tf0
TitleStructure of echovirus 18 in complex with neonatal Fc receptor
Components
  • (Echovirus 18 viral protein ...) x 4
  • Beta-2-microglobulin
  • IgG receptor FcRn large subunit p51
KeywordsVIRUS / Assembly
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / picornain 2A ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / beta-2-microglobulin binding / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / picornain 2A / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont-mediated suppression of host mRNA export from nucleus / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / symbiont genome entry into host cell via pore formation in plasma membrane / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / picornain 3C / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / T=pseudo3 icosahedral viral capsid / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / host cell cytoplasmic vesicle membrane / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / ribonucleoside triphosphate phosphatase activity / DAP12 signaling / late endosome membrane / nucleoside-triphosphate phosphatase / channel activity / ER-Phagosome pathway / early endosome membrane / monoatomic ion transmembrane transport / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / DNA replication / RNA helicase activity / endosome membrane / immune response / endocytosis involved in viral entry into host cell / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / focal adhesion / lysosomal membrane / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / Neutrophil degranulation / virion attachment to host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / proteolysis / : / DNA-templated transcription / RNA binding / extracellular exosome / extracellular region / zinc ion binding / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
Picornavirus coat protein VP4 superfamily / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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 / Class I Histocompatibility antigen, domains alpha 1 and 2 / 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) / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / MHC classes I/II-like antigen recognition protein / : / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / 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 / Immunoglobulin-like fold / 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
PALMITIC ACID / IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Echovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsMukhamedova, L. / Plevka, P.
Funding supportEuropean Union, 1items
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
DepositionNov 26, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4
A: Echovirus 18 viral protein 1
B: Echovirus 18 viral protein 2
G: IgG receptor FcRn large subunit p51
H: Beta-2-microglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,5807
Polymers136,3236
Non-polymers2561
Water1,67593
1
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4
A: Echovirus 18 viral protein 1
B: Echovirus 18 viral protein 2
G: IgG receptor FcRn large subunit p51
H: Beta-2-microglobulin
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)8,194,779420
Polymers8,179,394360
Non-polymers15,38560
Water6,485360
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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Echovirus 18 viral protein ... , 4 types, 4 molecules CDAB

#1: Protein Echovirus 18 viral protein 3 / VP3


Mass: 26143.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Echovirus 18 viral protein 4 / VP4


Mass: 7344.126 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Echovirus 18 viral protein 1 / VP1


Mass: 32564.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Echovirus 18 viral protein 2 / VP2


Mass: 28802.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echovirus E18
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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Protein , 2 types, 2 molecules GH

#5: Protein IgG receptor FcRn large subunit p51 / FcRn / IgG Fc fragment receptor transporter alpha chain / Neonatal Fc receptor


Mass: 29720.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGRT, FCRN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P55899
#6: Protein Beta-2-microglobulin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P61769

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Non-polymers , 2 types, 94 molecules

#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Echovirus E18 / Type: VIRUS / Entity ID: #1-#6 / Source: NATURAL
Molecular weightValue: 7.9 MDa / Experimental value: NO
Source (natural)Organism: Echovirus E18
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.5 / Details: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 54.48 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4533

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1crYOLO1.9.3particle selectionde novo trained model on partial datase
2EPUimage acquisition
4CTFFIND4CTF correction
7UCSF Chimera1.16model fitting
9RELION5.0.0initial Euler assignment
10RELION5.0.0final Euler assignment
12RELION5.0.03D reconstruction
13PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 80069
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16453 / Algorithm: FOURIER SPACE / Details: Ewald sphere correction applied for reconstruction / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: cross-correlation
Atomic model buildingPDB-ID: 7B5F

7b5f


Accession code: 7B5F / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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