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- EMDB-55863: Structure of echovirus 18 in complex with neonatal Fc receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-55863
TitleStructure of echovirus 18 in complex with neonatal Fc receptor
Map datamap
Sample
  • Virus: Echovirus E18
    • Protein or peptide: Echovirus 18 viral protein 3
    • Protein or peptide: Echovirus 18 viral protein 4
    • Protein or peptide: Echovirus 18 viral protein 1
    • Protein or peptide: Echovirus 18 viral protein 2
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulin
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsAssembly / VIRUS
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 / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / 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 / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / 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 / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / 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 neurogenesis / MHC class II protein complex / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / host cell cytoplasmic vesicle membrane / positive regulation of T cell mediated cytotoxicity / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / positive regulation of T cell activation / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / positive regulation of cellular senescence / tertiary granule lumen / MHC class II protein complex binding / ribonucleoside triphosphate phosphatase activity / T cell differentiation in thymus / DAP12 signaling / late endosome membrane / negative regulation of neuron projection development / nucleoside-triphosphate phosphatase / protein refolding / 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 / Golgi membrane / external side of plasma membrane / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / lysosomal membrane / cysteine-type endopeptidase activity / focal adhesion / viral RNA genome replication / RNA-directed RNA polymerase activity / Neutrophil degranulation / virion attachment to host cell / DNA-templated transcription / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / proteolysis / : / RNA binding / extracellular exosome / extracellular region
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
IgG receptor FcRn large subunit p51 / Beta-2-microglobulin / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus E18 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsMukhamedova L / Plevka P
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Particles of echovirus 18 open to release their genomes in vivo
Authors: Mukhamedova L / Plevka P / Buchta D / Fuzik T / Trebichalska Z / Novacek J / Levdansky Y / Moravcova J / Hrebik D / Tollefsrud TG / Andersen JT
History
DepositionNov 26, 2025-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55863.png

Downloads & links

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Map

FileDownload / File: emd_55863.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å		1.06 Å/pix.
x 512 pix.
= 543.232 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.22
Minimum - Maximum-11.873396 - 22.154066
Average (Standard dev.)0.000000000994555 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 543.232 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55863_msk_1.map
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AxesZYX

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Histogram (log scale)

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Half map: half2

Fileemd_55863_half_map_1.map
Annotationhalf2
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: half1

Fileemd_55863_half_map_2.map
Annotationhalf1
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Sample components

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Entire : Echovirus E18

EntireName: Echovirus E18
Components
  • Virus: Echovirus E18
    • Protein or peptide: Echovirus 18 viral protein 3
    • Protein or peptide: Echovirus 18 viral protein 4
    • Protein or peptide: Echovirus 18 viral protein 1
    • Protein or peptide: Echovirus 18 viral protein 2
    • Protein or peptide: IgG receptor FcRn large subunit p51
    • Protein or peptide: Beta-2-microglobulin
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 / 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

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Macromolecule #1: Echovirus 18 viral protein 3

MacromoleculeName: Echovirus 18 viral protein 3 / type: protein_or_peptide / ID: 1 / 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 #2: Echovirus 18 viral protein 4

MacromoleculeName: Echovirus 18 viral protein 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 7.344126 KDa
SequenceString:
GAQVSTQKTG AHETSLSAKG NSIIHYTNIN FYKDAASSAS NRQDIQQDPG KFTDPVKDLM IKTLPALN

UniProtKB: Genome polyprotein

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Macromolecule #3: Echovirus 18 viral protein 1

MacromoleculeName: Echovirus 18 viral protein 1 / type: protein_or_peptide / ID: 3 / 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 #4: Echovirus 18 viral protein 2

MacromoleculeName: Echovirus 18 viral protein 2 / type: protein_or_peptide / ID: 4 / 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 #5: IgG receptor FcRn large subunit p51

MacromoleculeName: IgG receptor FcRn large subunit p51 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.720383 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: AESHLSLLYH LTAVSSPAPG TPAFWVSGWL GPQQYLSYNS LRGEAEPCGA WVWENQVSWY WEKETTDLRI KEKLFLEAFK ALGGKGPYT LQGLLGCELG PDNTSVPTAK FALNGEEFMN FDLKQGTWGG DWPEALAISQ RWQQQDKAAN KELTFLLFSC P HRLREHLE ...String:
AESHLSLLYH LTAVSSPAPG TPAFWVSGWL GPQQYLSYNS LRGEAEPCGA WVWENQVSWY WEKETTDLRI KEKLFLEAFK ALGGKGPYT LQGLLGCELG PDNTSVPTAK FALNGEEFMN FDLKQGTWGG DWPEALAISQ RWQQQDKAAN KELTFLLFSC P HRLREHLE RGRGNLEWKE PPSMRLKARP SSPGFSVLTC SAFSFYPPEL QLRFLRNGLA AGTGQGDFGP NSDGSFHASS SL TVKSGDE HHYCCIVQHA GLAQPLRVEL

UniProtKB: IgG receptor FcRn large subunit p51

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Macromolecule #6: Beta-2-microglobulin

MacromoleculeName: Beta-2-microglobulin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.74816 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
IQRTPKIQVY SRHPAENGKS NFLNCYVSGF HPSDIEVDLL KNGERIEKVE HSDLSFSKDW SFYLLYYTEF TPTEKDEYAC RVNHVTLSQ PKIVKWDRDM

UniProtKB: Beta-2-microglobulin

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Macromolecule #7: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 7 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 93 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration2 mg/mL
BufferpH: 7.5 / Details: PBS
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 4533 / Average electron dose: 54.48 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 75000
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: 80069
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.0) / Details: Ewald sphere correction applied for reconstruction / Number images used: 16453
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7b5f


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF Chimera (ver. 1.16)
RefinementSpace: REAL / Protocol: OTHER / Target criteria: cross-correlation
Output model

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

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