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- PDB-6hbk: Echovirus 18 Open particle without one pentamer -

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Basic information

Entry
Database: PDB / ID: 6hbk
TitleEchovirus 18 Open particle without one pentamer
Components
  • Echovirus 18 capsid protein 1
  • Echovirus 18 capsid protein 2
  • Echovirus 18 capsid protein 3
KeywordsVIRUS / echovirus / echovirus 18 / open particle / O-particle / enterovirus / picornavirus / genome release
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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase ...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 / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / 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) / 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 / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Biological speciesEchovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Echovirus 18 capsid protein 1
g: Echovirus 18 capsid protein 2
f: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 3
d: Echovirus 18 capsid protein 2
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 3
a: Echovirus 18 capsid protein 2
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 3
X: Echovirus 18 capsid protein 2
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 3
U: Echovirus 18 capsid protein 2
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 3
R: Echovirus 18 capsid protein 2
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 3
O: Echovirus 18 capsid protein 2
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 3
L: Echovirus 18 capsid protein 2
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 3
I: Echovirus 18 capsid protein 2
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 3
F: Echovirus 18 capsid protein 2
C: Echovirus 18 capsid protein 2
B: Echovirus 18 capsid protein 3


Theoretical massNumber of molelcules
Total (without water)961,20733
Polymers961,20733
Non-polymers00
Water00
1
A: Echovirus 18 capsid protein 1
g: Echovirus 18 capsid protein 2
f: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 3
d: Echovirus 18 capsid protein 2
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 3
a: Echovirus 18 capsid protein 2
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 3
X: Echovirus 18 capsid protein 2
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 3
U: Echovirus 18 capsid protein 2
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 3
R: Echovirus 18 capsid protein 2
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 3
O: Echovirus 18 capsid protein 2
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 3
L: Echovirus 18 capsid protein 2
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 3
I: Echovirus 18 capsid protein 2
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 3
F: Echovirus 18 capsid protein 2
C: Echovirus 18 capsid protein 2
B: Echovirus 18 capsid protein 3
x 5


Theoretical massNumber of molelcules
Total (without water)4,806,033165
Polymers4,806,033165
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5

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Components

#1: Protein
Echovirus 18 capsid protein 1


Mass: 32564.445 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635
#2: Protein
Echovirus 18 capsid protein 2


Mass: 26143.783 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635
#3: Protein
Echovirus 18 capsid protein 3


Mass: 28674.199 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635

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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: all / Source: NATURAL
Molecular weightValue: 7.20 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: 340 nm / Triangulation number (T number): 1
Buffer solutionpH: 6
Buffer component
IDConc.NameFormulaBuffer-ID
137.5 mM2-(N-Morpholino)ethanesulfonic acidMES1
25 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris1
325 mMsodium chlorideNaCl1
SpecimenConc.: 0.5 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 FIELD / Nominal magnification: 75000 X / Calibrated magnification: 79575 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 651 nm / Calibrated defocus max: 3282 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 45.2 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6331
Details: Images were collected in movie-mode at 39 frames per second
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Gautomatch8particle selection
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimera1.11.2model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12RELION2.13D reconstruction
13PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 509565
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3563 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 131.32 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor / Details: Group B-factor refinement
Atomic model buildingPDB-ID: 6HBH

6hbh

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