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- PDB-6hbl: Echovirus 18 Open particle without three pentamers -

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Basic information

Entry
Database: PDB / ID: 6hbl
TitleEchovirus 18 Open particle without three pentamers
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
Function / homology
Function and homology information


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 / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell ...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 / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / induction by virus of host autophagy / suppression by virus of host gene expression / RNA-directed RNA polymerase / protein complex oligomerization / ion channel activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / 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 ...Peptidase C3, picornavirus core protein 2A / Picornavirus/Calicivirus coat protein / P-loop containing nucleoside triphosphate hydrolase / 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 / Poliovirus core protein 3a, soluble domain / Picornavirus coat protein VP4 superfamily / Viral coat protein subunit / 3C cysteine protease (picornain 3C) / 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 capsid protein / Picornavirus core protein 2A / RNA helicase / RNA dependent RNA polymerase
Genome polyprotein
Biological speciesEchovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 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.
Validation Report
SummaryFull reportAbout validation report
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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Assembly

Deposited unit
A: Echovirus 18 capsid protein 1
q: Echovirus 18 capsid protein 1
r: Echovirus 18 capsid protein 2
s: Echovirus 18 capsid protein 3
n: Echovirus 18 capsid protein 1
o: Echovirus 18 capsid protein 2
p: Echovirus 18 capsid protein 3
k: Echovirus 18 capsid protein 1
l: Echovirus 18 capsid protein 2
m: Echovirus 18 capsid protein 3
h: Echovirus 18 capsid protein 1
i: Echovirus 18 capsid protein 2
j: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
f: Echovirus 18 capsid protein 2
g: Echovirus 18 capsid protein 3
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 2
d: Echovirus 18 capsid protein 3
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 2
a: Echovirus 18 capsid protein 3
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 2
X: Echovirus 18 capsid protein 3
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 2
U: Echovirus 18 capsid protein 3
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 2
R: Echovirus 18 capsid protein 3
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 2
O: Echovirus 18 capsid protein 3
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 2
L: Echovirus 18 capsid protein 3
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 2
I: Echovirus 18 capsid protein 3
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 2
F: Echovirus 18 capsid protein 3
C: Echovirus 18 capsid protein 3
B: Echovirus 18 capsid protein 2


Theoretical massNumber of molelcules
Total (without water)1,312,65845
Polymers1,312,65845
Non-polymers00
Water0
1
A: Echovirus 18 capsid protein 1
q: Echovirus 18 capsid protein 1
r: Echovirus 18 capsid protein 2
s: Echovirus 18 capsid protein 3
n: Echovirus 18 capsid protein 1
o: Echovirus 18 capsid protein 2
p: Echovirus 18 capsid protein 3
k: Echovirus 18 capsid protein 1
l: Echovirus 18 capsid protein 2
m: Echovirus 18 capsid protein 3
h: Echovirus 18 capsid protein 1
i: Echovirus 18 capsid protein 2
j: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
f: Echovirus 18 capsid protein 2
g: Echovirus 18 capsid protein 3
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 2
d: Echovirus 18 capsid protein 3
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 2
a: Echovirus 18 capsid protein 3
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 2
X: Echovirus 18 capsid protein 3
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 2
U: Echovirus 18 capsid protein 3
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 2
R: Echovirus 18 capsid protein 3
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 2
O: Echovirus 18 capsid protein 3
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 2
L: Echovirus 18 capsid protein 3
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 2
I: Echovirus 18 capsid protein 3
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 2
F: Echovirus 18 capsid protein 3
C: Echovirus 18 capsid protein 3
B: Echovirus 18 capsid protein 2

A: Echovirus 18 capsid protein 1
q: Echovirus 18 capsid protein 1
r: Echovirus 18 capsid protein 2
s: Echovirus 18 capsid protein 3
n: Echovirus 18 capsid protein 1
o: Echovirus 18 capsid protein 2
p: Echovirus 18 capsid protein 3
k: Echovirus 18 capsid protein 1
l: Echovirus 18 capsid protein 2
m: Echovirus 18 capsid protein 3
h: Echovirus 18 capsid protein 1
i: Echovirus 18 capsid protein 2
j: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
f: Echovirus 18 capsid protein 2
g: Echovirus 18 capsid protein 3
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 2
d: Echovirus 18 capsid protein 3
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 2
a: Echovirus 18 capsid protein 3
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 2
X: Echovirus 18 capsid protein 3
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 2
U: Echovirus 18 capsid protein 3
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 2
R: Echovirus 18 capsid protein 3
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 2
O: Echovirus 18 capsid protein 3
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 2
L: Echovirus 18 capsid protein 3
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 2
I: Echovirus 18 capsid protein 3
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 2
F: Echovirus 18 capsid protein 3
C: Echovirus 18 capsid protein 3
B: Echovirus 18 capsid protein 2

A: Echovirus 18 capsid protein 1
q: Echovirus 18 capsid protein 1
r: Echovirus 18 capsid protein 2
s: Echovirus 18 capsid protein 3
n: Echovirus 18 capsid protein 1
o: Echovirus 18 capsid protein 2
p: Echovirus 18 capsid protein 3
k: Echovirus 18 capsid protein 1
l: Echovirus 18 capsid protein 2
m: Echovirus 18 capsid protein 3
h: Echovirus 18 capsid protein 1
i: Echovirus 18 capsid protein 2
j: Echovirus 18 capsid protein 3
e: Echovirus 18 capsid protein 1
f: Echovirus 18 capsid protein 2
g: Echovirus 18 capsid protein 3
b: Echovirus 18 capsid protein 1
c: Echovirus 18 capsid protein 2
d: Echovirus 18 capsid protein 3
Y: Echovirus 18 capsid protein 1
Z: Echovirus 18 capsid protein 2
a: Echovirus 18 capsid protein 3
V: Echovirus 18 capsid protein 1
W: Echovirus 18 capsid protein 2
X: Echovirus 18 capsid protein 3
S: Echovirus 18 capsid protein 1
T: Echovirus 18 capsid protein 2
U: Echovirus 18 capsid protein 3
P: Echovirus 18 capsid protein 1
Q: Echovirus 18 capsid protein 2
R: Echovirus 18 capsid protein 3
M: Echovirus 18 capsid protein 1
N: Echovirus 18 capsid protein 2
O: Echovirus 18 capsid protein 3
J: Echovirus 18 capsid protein 1
K: Echovirus 18 capsid protein 2
L: Echovirus 18 capsid protein 3
G: Echovirus 18 capsid protein 1
H: Echovirus 18 capsid protein 2
I: Echovirus 18 capsid protein 3
D: Echovirus 18 capsid protein 1
E: Echovirus 18 capsid protein 2
F: Echovirus 18 capsid protein 3
C: Echovirus 18 capsid protein 3
B: Echovirus 18 capsid protein 2


Theoretical massNumber of molelcules
Total (without water)3,937,975135
Polymers3,937,975135
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation2
Buried area302370 Å2
ΔGint-1826 kcal/mol
Surface area295460 Å2
MethodPISA

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Components

#1: Protein/peptide
Echovirus 18 capsid protein 1


Mass: 32564.445 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / References: UniProt: Q8V635
#2: Protein/peptide
Echovirus 18 capsid protein 2


Mass: 28802.328 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / References: UniProt: Q8V635
#3: Protein/peptide
Echovirus 18 capsid protein 3


Mass: 26143.783 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Echovirus E18 / 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: 1, 2, 3 / Source: NATURAL
Molecular weightValue: 6.33 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

Buffer-ID: 1

IDConc.NameFormula
137.5 mM2-(N-Morpholino)ethanesulfonic acidMES
25 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris
325 mMsodium chlorideNaClSodium chloride
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 FIELDBright-field microscopy / 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 / 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 Chimera1.11model fitting
9PHENIX1.13model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 13635 / Algorithm: BACK PROJECTION / Num. of class averages: 2 / Symmetry type: POINT
Atomic model buildingB value: 92.45 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factor
Atomic model buildingPDB-ID: 6HBH

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