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- PDB-6hbg: Echovirus 18 native particle -

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Basic information

Entry
Database: PDB / ID: 6hbg
TitleEchovirus 18 native particle
Components(Echovirus 18 viral protein ...) x 4
KeywordsVIRUS / echovirus / echovirus 18 / native particle / enterovirus / picornavirus
Function / 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
Specimen sourceEchovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsBuchta, D. / Fuzik, T. / Hrebik, D. / Levdansky, Y. / Moravcova, J. / Plevka, P.
Funding supportCzech Republic , 1 items
OrganizationGrant numberCountry
European Research Council335855Czech 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 10, 2018 / Release: Mar 20, 2019

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Assembly

Deposited unit
A: Echovirus 18 viral protein 1
B: Echovirus 18 viral protein 2
C: Echovirus 18 viral protein 3
D: Echovirus 18 viral protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3936
Polyers94,9864
Non-polymers4082
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)20170
ΔGint (kcal/M)-101
Surface area (Å2)30430
MethodPISA

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Components

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Echovirus 18 viral protein ... , 4 types, 4 molecules ABCD

#1: Protein/peptide Echovirus 18 viral protein 1


Mass: 32564.445 Da / Num. of mol.: 1 / Source: (natural) Echovirus E18 / Cell line: GMK
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein/peptide Echovirus 18 viral protein 2


Mass: 28802.328 Da / Num. of mol.: 1 / Source: (natural) Echovirus E18 / Cell line: GMK
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein/peptide Echovirus 18 viral protein 3


Mass: 26143.783 Da / Num. of mol.: 1 / Source: (natural) Echovirus E18 / Cell line: GMK
References: UniProt: Q8V635, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein/peptide Echovirus 18 viral protein 4


Mass: 7475.322 Da / Num. of mol.: 1 / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Formula: C16H32O2 / Palmitic acid
#6: Chemical ChemComp-GUN / GUANINE


Mass: 151.126 Da / Num. of mol.: 1 / Formula: C5H5N5O / Guanine

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Echovirus E18 / Type: VIRUS / Entity ID: 1, 2, 3, 4 / Source: NATURAL
Molecular weightValue: 7.63 MDa / Experimental value: NO
Source (natural)Organism: Echovirus E18 / Strain: Metcalf
Details of virusEmpty: NO / Enveloped: NO / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 320 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer component

Buffer-ID: 1

IDConc. (mg/ml)NameFormula
120 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris
2100 mMsodium chlorideNaCl
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Calibrated magnification: 79725 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 660 nm / Calibrated defocus max: 3429 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46.8 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 938
Image scansSampling size: 14 microns / Width: 4096 / Height: 4096

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Processing

SoftwareName: PHENIX / Version: (1.14rc1_3161: ???) / Classification: refinement
EM software
IDNameVersionCategory
1Gautomatch8particle selection
2EPUimage acquisition
7Coot0.8.7model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 42863
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10062 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingDetails: Reciprocal space refinement of atom positions and group B-factors
B value: 82.8 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-factors
Atomic model buildingPDB-ID: 2X5I
RefinementResolution: 3.16→263.079 Å / SU ML: 0.6 / σ(F): 0.13 / Phase error: 36.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3245144935 %
Rwork0.3234--
obs0.323428979099.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealNumber
f_bond_d0.00431440
f_angle_d0.73642885
f_dihedral_angle_d10.27411285
f_chiral_restr0.054785
f_plane_restr0.0075495

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