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- EMDB-33502: Echo 18 at pH5.5 -

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Basic information

Entry
Database: EMDB / ID: EMD-33502
TitleEcho 18 at pH5.5
Map data
Sample
  • Virus: Echovirus E18
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID
Biological speciesEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsLiu CC / Qu X
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences81971922 China
CitationJournal: mBio / Year: 2022
Title: Human FcRn Is a Two-in-One Attachment-Uncoating Receptor for Echovirus 18.
Authors: Xiangpeng Chen / Xiao Qu / Congcong Liu / Yong Zhang / Guigen Zhang / Pu Han / Yali Duan / Qi Li / Liang Wang / Wenjing Ruan / Peiyi Wang / Wensheng Wei / George F Gao / Xin Zhao / Zhengde Xie /
Abstract: Virus-receptor interactions determine viral host range and tissue tropism. CD55 and human neonatal Fc receptor (FcRn) were found to be the binding and uncoating receptors for some of the echovirus- ...Virus-receptor interactions determine viral host range and tissue tropism. CD55 and human neonatal Fc receptor (FcRn) were found to be the binding and uncoating receptors for some of the echovirus-related enterovirus species B serotypes in our previous study. Echovirus 18 (E18), as a member of enterovirus species B, is a significant causative agent of aseptic meningitis and viral encephalitis in children. However, it does not use CD55 as a critical host factor. We conducted CRISPR/Cas9 knockout screening to determine the receptors and entry mechanisms and identified FcRn working as a dual-function receptor for E18. Knockout of and , which encode the two subunits of FcRn, prevented infection by E18 and other echoviruses in the same physiological cluster. We then elucidated the underlying molecular mechanism of receptor recognition by E18 using cryogenic electron microscopy. The binding of the FCGRT subunit to the canyon region rotates the residues around the pocket, triggering the release of the pocket factor as observed for other enterovirus species B members. E18 is a member of enterovirus species B. As one of the most common enterovirus serotypes in nonpolio enterovirus detection, it easily infects children and causes various clinical symptoms. Aseptic meningitis and viral encephalitis are the most commonly reported syndromes associated with E18. No effective antiviral drugs or approved vaccines are available. Previous studies showed that CD55 and FcRn were the binding and uncoating receptors for some echoviruses. However, we found that CD55 is not the critical host factor for E18. Thus, we want to determine the receptors and elucidate the entry mechanism of E18. Our findings reveal that FcRn is a two-in-one attachment-uncoating receptor for E18.
History
DepositionMay 30, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33502.png

Downloads & links

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Map

FileDownload / File: emd_33502.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.41 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.15443057 - 0.270942
Average (Standard dev.)0.004331864 (±0.02212469)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33502_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33502_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_33502_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
    • Protein or peptide: VP4
  • Ligand: PALMITIC ACID

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 31.308102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDNQDRTVAN TQPSGPSNSK EIPALTAVET GHTSQVDPSD TLQTRHVVNF HSRSESTVEN FMGRAACVFM DQYKLNGEET STDNFAVWT INVREMAQLR RKCELFTYMR FDIEMTMVIT SCQDQGTQLE QDMPVLTHQI MYVPPGGPIP AKVDSYEWQT S TNPSVFWT ...String:
GDNQDRTVAN TQPSGPSNSK EIPALTAVET GHTSQVDPSD TLQTRHVVNF HSRSESTVEN FMGRAACVFM DQYKLNGEET STDNFAVWT INVREMAQLR RKCELFTYMR FDIEMTMVIT SCQDQGTQLE QDMPVLTHQI MYVPPGGPIP AKVDSYEWQT S TNPSVFWT EGNAPARMSI PFISVGNAYS LFYDGWSHFT QDGTYGYTTL NAMGKLFVRH VNKSSPHQIT STIRVYFKPK HI KAWVPRP PRLCPYINKG DVNFVVTEVT DARKSITDTP

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 28.805348 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDKEATAE DQPTQPDVAT CRFYTLESVQ WEKSSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTST TFPATELTTE EEPHVFTSDS I TGKKVQAA ...String:
SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDKEATAE DQPTQPDVAT CRFYTLESVQ WEKSSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTST TFPATELTTE EEPHVFTSDS I TGKKVQAA VCNAGMGVGV GNLTIFPHQW INLRTNNSAT IVMPYINSVP MDNMFRHYNF TLMIIPFAPL NFNEGATAYV PV TVTIAPM YAEYNGLRLA STQ

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 26.134842 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GVPVLNTPGS TQFLTSDDFQ SPSAMPQFDE TPEMHIPGEV RNLMEMAEVD SVVPVNNITG KTKSMEAYQI AVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPSSRKDA MLGTHIIWDI G LQSSCVLC ...String:
GVPVLNTPGS TQFLTSDDFQ SPSAMPQFDE TPEMHIPGEV RNLMEMAEVD SVVPVNNITG KTKSMEAYQI AVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPSSRKDA MLGTHIIWDI G LQSSCVLC VPWISQSHYR MVQQDPYTSA GYITCWYQTN IVVPPGAPTS CDVLCFASAC NDFSVRLLRD TPFMAQPGKL Q

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Macromolecule #4: VP4

MacromoleculeName: VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 7.502346 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGAQVSTQKT GAHETSLNAK GNSIIHYTNI NFYKDAASSA SNRQELQQDP GKFTDPVKDL MVKTLPALN

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Macromolecule #5: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 5 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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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: 5.5
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 457 / Average exposure time: 0.09 sec. / Average electron dose: 1.025 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 9905
Startup modelType of model: EMDB MAP
EMDB ID:

33499

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0.8)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.08) / Number images used: 9905
FSC plot (resolution estimation)

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