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- EMDB-0183: Echovirus 18 empty particle -

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Basic information

Entry
Database: EMDB / ID: EMD-0183
TitleEchovirus 18 empty particle
Map dataEchovirus 18 empty particle
Sample
  • Virus: Echovirus E18
    • Protein or peptide: Viral protein 1
    • Protein or peptide: Viral protein 2
    • Protein or peptide: Viral protein 3
Keywordsechovirus / echovirus 18 / empty particle / B-particle / enterovirus / picornavirus / VIRUS
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 / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...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 / 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 / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / 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: 3.16 Å
AuthorsBuchta D / Fuzik T
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
European Research Council335855 Czech Republic
CitationJournal: Nat Commun / Year: 2019
Title: Enterovirus particles expel capsid pentamers to enable genome release.
Authors: David Buchta / Tibor Füzik / Dominik Hrebík / Yevgen Levdansky / Lukáš Sukeník / Liya Mukhamedova / Jana Moravcová / Robert Vácha / Pavel Plevka /
Abstract: Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for ...Viruses from the genus Enterovirus are important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for genome release. However, the mechanism of enterovirus uncoating is not well understood. Here, we use cryo-electron microscopy to visualize virions of human echovirus 18 in the process of genome release. We discover that the exit of the RNA from the particle of echovirus 18 results in a loss of one, two, or three adjacent capsid-protein pentamers. The opening in the capsid, which is more than 120 Å in diameter, enables the release of the genome without the need to unwind its putative double-stranded RNA segments. We also detect capsids lacking pentamers during genome release from echovirus 30. Thus, our findings uncover a mechanism of enterovirus genome release that could become target for antiviral drugs.
History
DepositionAug 10, 2018-
Header (metadata) releaseMar 20, 2019-
Map releaseMar 20, 2019-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hbj
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hbj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0183.png

Downloads & links

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Map

FileDownload / File: emd_0183.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEchovirus 18 empty particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 350 pix.
= 372.05 Å		1.06 Å/pix.
x 350 pix.
= 372.05 Å		1.06 Å/pix.
x 350 pix.
= 372.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.063 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-0.36768115 - 0.6925562
Average (Standard dev.)0.005743135 (±0.047577202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-175-175-175
Dimensions350350350
Spacing350350350
CellA=B=C: 372.05 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0631.0631.063
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z372.050372.050372.050
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS350350350
D min/max/mean-0.3680.6930.006

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Supplemental data

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Half map: Echovirus 18 empty particle half-map

Fileemd_0183_half_map_1.map
AnnotationEchovirus 18 empty particle half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Echovirus 18 empty particle half-map

Fileemd_0183_half_map_2.map
AnnotationEchovirus 18 empty particle half-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: Viral protein 1
    • Protein or peptide: Viral protein 2
    • Protein or peptide: Viral protein 3

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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 / Sci species strain: Metcalf / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.24 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 330.0 Å / T number (triangulation number): 1

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Macromolecule #1: Viral protein 1

MacromoleculeName: Viral protein 1 / 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: Viral protein 2

MacromoleculeName: 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: Viral protein 3

MacromoleculeName: 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.0 mg/mL
BufferpH: 5.8
Component:
ConcentrationFormulaName
10.0 mMNa2HPO4sodium phosphate dibasic
1.8 mMKH2PO4monobasic potassium phosphate
137.0 mMNaClsodium chloride
2.7 mMKClpotassium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 16784 / Average exposure time: 1.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.8160000000000003 µm / Calibrated defocus min: 0.357 µm / Calibrated magnification: 79725 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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: 472267
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6hbh


Details: Echovirus 18 A-particle
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 8511
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 6241 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsReciprocal space refinement of atom positions and group B-factors
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT / Overall B value: 117.89 / Target criteria: R-factors
Output model

PDB-6hbj:
Echovirus 18 empty particle

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