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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 / 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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : ...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 / endocytosis involved in viral entry into host cell / cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Jelly Rolls - #20 / 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 ...Jelly Rolls - #20 / 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) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / 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 / Jelly Rolls / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
GUANINE / PALMITIC ACID / Genome polyprotein
Similarity search - Component
Biological speciesEchovirus 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 support Czech Republic, 1items
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, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Derived calculations
Category: em_admin / pdbx_database_proc ...em_admin / pdbx_database_proc / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _em_admin.last_update / _pdbx_struct_assembly.method_details ..._em_admin.last_update / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Dec 11, 2019Group: Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB
Revision 1.3Aug 4, 2021Group: Other / Category: symmetry / Item: _symmetry.space_group_name_H-M

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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
Polymers94,9864
Non-polymers4082
Water0
1
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
x 60


Theoretical massNumber of molelcules
Total (without water)5,723,606360
Polymers5,699,153240
Non-polymers24,453120
Water0
TypeNameSymmetry operationNumber
identity operation1
point symmetry operation59
Buried area20170 Å2
ΔGint-101 kcal/mol
Surface area30430 Å2
MethodChimera

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Components

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

#1: Protein Echovirus 18 viral protein 1


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


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


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


Mass: 7475.322 Da / Num. of mol.: 1 / Source method: isolated from a natural source / 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 / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#6: Chemical ChemComp-GUN / GUANINE / Guanine


Mass: 151.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5O

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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-#4 / Source: NATURAL
Molecular weightValue: 7.63 MDa / Experimental value: NO
Source (natural)Organism: Echovirus E18 / Strain: Metcalf
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: Capsid / Diameter: 320 nm / Triangulation number (T number): 1
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris1
2100 mMsodium chlorideNaClSodium chloride1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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 X / Calibrated magnification: 79725 X / 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 / Specimen holder 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 µm / 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 buildingB value: 82.8 / Protocol: FLEXIBLE FIT / Space: RECIPROCAL / Target criteria: R-factors
Details: Reciprocal space refinement of atom positions and group B-factors
Atomic model buildingPDB-ID: 2X5I

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
Rfree0.3245 14493 5 %
Rwork0.3234 --
obs0.3234 289790 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00431440
X-RAY DIFFRACTIONf_angle_d0.73642885
X-RAY DIFFRACTIONf_dihedral_angle_d10.27411285
X-RAY DIFFRACTIONf_chiral_restr0.054785
X-RAY DIFFRACTIONf_plane_restr0.0075495

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