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- EMDB-0181: Echovirus 18 native particle -

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Basic information

Entry
Database: EMDB / Id: 181
TitleEchovirus 18 native particle
Map dataEchovirus 18 native particle
SampleEchovirus E18:
virus / (Echovirus 18 viral protein ...) x 4 / (ligand) x 2
Func homologyPeptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid ...Peptidase C3, picornavirus core protein 2A / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, catalytic domain / AAA+ ATPase domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA helicase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Picornavirus 2B protein / Picornavirus core protein 2A / RNA dependent RNA polymerase / 3C cysteine protease (picornain 3C) / picornavirus capsid protein / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / T=pseudo3 icosahedral viral capsid / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / RNA-directed RNA polymerase / induction by virus of host autophagy / suppression by virus of host gene expression / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein
Function and homology information
SourceEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsBuchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P
CitationJournal: Nat Commun / Year: 2019
Title: Enterovirus particles expel capsid pentamers to enable genome release.
P-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.
Validation ReportPDB-ID: 6hbg

SummaryFull reportAbout validation report
DateDeposition: Aug 10, 2018 / Header (metadata) release: Sep 5, 2018 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hbg
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6hbg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_0181.map.gz (map file in CCP4 format, 171501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
350 pix
1.06 Å/pix.
= 372.05 Å
350 pix
1.06 Å/pix.
= 372.05 Å
350 pix
1.06 Å/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
Contour Level:0.15 (by author), 0.15 (movie #1):
Minimum - Maximum-0.42712843 - 0.58722675
Average (Standard dev.)0.0024383 (0.045418993)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions350350350
Origin-175.0-175.0-175.0
Limit174.0174.0174.0
Spacing350350350
CellA=B=C: 372.05 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-175-175-175
NC/NR/NS350350350
D min/max/mean-0.4270.5870.002

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Supplemental data

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Sample components

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Entire Echovirus E18

EntireName: Echovirus E18 / Number of components: 7

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Component #1: virus, Echovirus E18

VirusName: Echovirus E18 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 7.63 MDa
SpeciesSpecies: Echovirus E18 / Strain: Metcalf
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: Capsid / Diameter: 320.0 Å / T number(triangulation number): 1

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Component #2: protein, Echovirus 18 viral protein 1

ProteinName: Echovirus 18 viral protein 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.564445 kDa
SourceSpecies: Echovirus E18

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Component #3: protein, Echovirus 18 viral protein 2

ProteinName: Echovirus 18 viral protein 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.802328 kDa
SourceSpecies: Echovirus E18

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Component #4: protein, Echovirus 18 viral protein 3

ProteinName: Echovirus 18 viral protein 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.143783 kDa
SourceSpecies: Echovirus E18

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Component #5: protein, Echovirus 18 viral protein 4

ProteinName: Echovirus 18 viral protein 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.475322 kDa
SourceSpecies: Echovirus E18

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Component #6: ligand, PALMITIC ACID

LigandName: PALMITIC ACID / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.256424 kDa

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Component #7: ligand, GUANINE

LigandName: GUANINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.151126 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/ml / Ph: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 46.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal), 79725.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 938 / Sampling size: 14 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 10062
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: R-factors / Refinement space: RECIPROCAL
Details: Reciprocal space refinement of atom positions and group B-factors
Input PDB model: 2X5I
Overall bvalue: 82.8
Output model

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