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- EMDB-12028: Structure of echovirus 18 in complex with neonatal Fc receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-12028
TitleStructure of echovirus 18 in complex with neonatal Fc receptor
Map dataThe complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin
Sample
  • Complex: Structure of echovirus 18 in complex with neonatal Fc receptor
    • Complex: Echovirus 18 native virion
      • 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
    • Complex: Heterodimer of neonatal Fc Receptor and beta-2-microglobulin
      • Protein or peptide: IgG receptor FcRn large subunit p51
      • Protein or peptide: Beta-2-microglobulin
  • Ligand: PALMITIC ACID
  • Ligand: GUANINE
Keywordscomplex / echovirus 18 virion / neonatal fc receptor / fcrn / beta-2-microglobulin / microglobulin / pocket factor / VIRUS
Function / homology
Function and homology information


IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion ...IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor / IgG binding / beta-2-microglobulin binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / symbiont genome entry into host cell via pore formation in plasma membrane / peptide antigen assembly with MHC class II protein complex / picornain 3C / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / T=pseudo3 icosahedral viral capsid / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / host cell cytoplasmic vesicle membrane / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / nucleoside-triphosphate phosphatase / negative regulation of neuron projection development / channel activity / ER-Phagosome pathway / protein refolding / early endosome membrane / monoatomic ion transmembrane transport / protein homotetramerization / amyloid fibril formation / 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 / symbiont-mediated activation of host autophagy / lysosomal membrane / external side of plasma membrane / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / focal adhesion / RNA-directed RNA polymerase activity / DNA-templated transcription / Neutrophil degranulation / virion attachment to host cell / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / ATP hydrolysis activity / proteolysis / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion 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) / Class I Histocompatibility antigen, domains alpha 1 and 2 / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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: 2.9 Å
AuthorsBuchta D / Levdansky Y
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Grant Agency of the Czech RepublicGX19-25982X Czech Republic
CitationJournal: To Be Published
Title: Structure of echovirus 18 in complex with neonatal Fc receptor
Authors: Buchta D / Levdansky Y / Fuzik T / Mukhamedova L / Moravcova J / Hrebik D / Andersen JT / Plevka P
History
DepositionDec 3, 2020-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7b5f
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7b5f
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12028.png

Downloads & links

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Map

FileDownload / File: emd_12028.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 440 pix.
= 466.84 Å		1.06 Å/pix.
x 440 pix.
= 466.84 Å		1.06 Å/pix.
x 440 pix.
= 466.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.061 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.03
Minimum - Maximum-0.123589724 - 0.22674704
Average (Standard dev.)0.0023330182 (±0.014662678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-220-220-220
Dimensions440440440
Spacing440440440
CellA=B=C: 466.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z466.840466.840466.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-220-220-220
NC/NR/NS440440440
D min/max/mean-0.1240.2270.002

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Supplemental data

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Half map: The complex of echovirus 18 virion with heterodimer...

Fileemd_12028_half_map_1.map
AnnotationThe complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The complex of echovirus 18 virion with heterodimer...

Fileemd_12028_half_map_2.map
AnnotationThe complex of echovirus 18 virion with heterodimer of neonatal Fc receptor (FcRn) and beta-2-microglobulin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of echovirus 18 in complex with neonatal Fc receptor

EntireName: Structure of echovirus 18 in complex with neonatal Fc receptor
Components
  • Complex: Structure of echovirus 18 in complex with neonatal Fc receptor
    • Complex: Echovirus 18 native virion
      • 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
    • Complex: Heterodimer of neonatal Fc Receptor and beta-2-microglobulin
      • Protein or peptide: IgG receptor FcRn large subunit p51
      • Protein or peptide: Beta-2-microglobulin
  • Ligand: PALMITIC ACID
  • Ligand: GUANINE

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Supramolecule #1: Structure of echovirus 18 in complex with neonatal Fc receptor

SupramoleculeName: Structure of echovirus 18 in complex with neonatal Fc receptor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 2.49 MDa

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Supramolecule #2: Echovirus 18 native virion

SupramoleculeName: Echovirus 18 native virion / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Echovirus E18

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Supramolecule #3: Heterodimer of neonatal Fc Receptor and beta-2-microglobulin

SupramoleculeName: Heterodimer of neonatal Fc Receptor and beta-2-microglobulin
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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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 / Tissue: Kidney
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 / Organ: Kidney
Molecular weightTheoretical: 7.475322 KDa
SequenceString:
MGAQVSTQKT GAHETSLSAK GNSIIHYTNI NFYKDAASSA SNRQDIQQDP GKFTDPVKDL MIKTLPALN

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 / Tissue: Kidney
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 / Tissue: Kidney
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: unidentified baculovirus
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: unidentified baculovirus
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: GUANINE

MacromoleculeName: GUANINE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GUN
Molecular weightTheoretical: 151.126 Da
Chemical component information

ChemComp-GUN:
GUANINE

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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

Concentration2.00 mg/mL
BufferpH: 7.3
Component:
ConcentrationFormulaName
10.0 mMTris2-Amino-2-(hydroxymethyl)-1,3-propanediol
118.5 mMNaClsodium chloride
1.35 mMKClpotassium chloride
4.0 mMNa2HPO4Disodium phosphate
1.0 mMKH2PO4Monopotassium phosphate

Details: Mixed in 1:1 volume ratio {20 mM Tris (pH=7.2), 100 mM NaCl} and {8 mM Na2HPO4, 2 mM KH2PO4 (pH=7.4), 137 mM NaCl, 2.7 mM KCl}=PBS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 4531 / Average exposure time: 1.27 sec. / Average electron dose: 54.48 e/Å2 / Details: Images were collected in movie-mode at 50 frames.
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: 125031
Startup model#0 - Type of model: EMDB MAP
#0 - EMDB ID:

0183


#0 - Details: Echovirus 18 empty particle / #1 - Type of model: PDB ENTRY
#1 - PDB model - PDB ID:

1exu


#2 - Type of model: PDB ENTRY
#2 - PDB model - PDB ID:

6hbg

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 13062
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementTarget criteria: R-factors
Output model

PDB-7b5f:
Structure of echovirus 18 in complex with neonatal Fc receptor

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