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- PDB-6hht: Echovirus 18 Open particle without two pentamers -

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Basic information

Entry
Database: PDB / ID: 6hht
TitleEchovirus 18 Open particle without two 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 / 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 / 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
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) ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEchovirus E18
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 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 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Structure summary / Category: em_admin / pdbx_database_proc / struct
Item: _em_admin.last_update / _em_admin.title / _struct.title

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Assembly

Deposited unit
A1: Echovirus 18 capsid protein 1
V1: Echovirus 18 capsid protein 1
W1: Echovirus 18 capsid protein 2
X1: Echovirus 18 capsid protein 3
S1: Echovirus 18 capsid protein 1
T1: Echovirus 18 capsid protein 2
U1: Echovirus 18 capsid protein 3
P1: Echovirus 18 capsid protein 1
Q1: Echovirus 18 capsid protein 2
R1: Echovirus 18 capsid protein 3
M1: Echovirus 18 capsid protein 1
N1: Echovirus 18 capsid protein 2
O1: Echovirus 18 capsid protein 3
J1: Echovirus 18 capsid protein 1
K1: Echovirus 18 capsid protein 2
L1: Echovirus 18 capsid protein 3
G1: Echovirus 18 capsid protein 1
H1: Echovirus 18 capsid protein 2
I1: Echovirus 18 capsid protein 3
D1: Echovirus 18 capsid protein 1
E1: Echovirus 18 capsid protein 2
F1: Echovirus 18 capsid protein 3
C1: Echovirus 18 capsid protein 3
B1: Echovirus 18 capsid protein 2
A2: Echovirus 18 capsid protein 1
w2: Echovirus 18 capsid protein 1
x2: Echovirus 18 capsid protein 2
y2: Echovirus 18 capsid protein 3
t2: Echovirus 18 capsid protein 1
u2: Echovirus 18 capsid protein 2
v2: Echovirus 18 capsid protein 3
q2: Echovirus 18 capsid protein 1
r2: Echovirus 18 capsid protein 2
s2: Echovirus 18 capsid protein 3
n2: Echovirus 18 capsid protein 1
o2: Echovirus 18 capsid protein 2
p2: Echovirus 18 capsid protein 3
k2: Echovirus 18 capsid protein 1
l2: Echovirus 18 capsid protein 2
m2: Echovirus 18 capsid protein 3
h2: Echovirus 18 capsid protein 1
i2: Echovirus 18 capsid protein 2
j2: Echovirus 18 capsid protein 3
e2: Echovirus 18 capsid protein 1
f2: Echovirus 18 capsid protein 2
g2: Echovirus 18 capsid protein 3
b2: Echovirus 18 capsid protein 1
c2: Echovirus 18 capsid protein 2
d2: Echovirus 18 capsid protein 3
Y2: Echovirus 18 capsid protein 1
Z2: Echovirus 18 capsid protein 2
a2: Echovirus 18 capsid protein 3
V2: Echovirus 18 capsid protein 1
W2: Echovirus 18 capsid protein 2
X2: Echovirus 18 capsid protein 3
S2: Echovirus 18 capsid protein 1
T2: Echovirus 18 capsid protein 2
U2: Echovirus 18 capsid protein 3
P2: Echovirus 18 capsid protein 1
Q2: Echovirus 18 capsid protein 2
R2: Echovirus 18 capsid protein 3
M2: Echovirus 18 capsid protein 1
N2: Echovirus 18 capsid protein 2
O2: Echovirus 18 capsid protein 3
J2: Echovirus 18 capsid protein 1
K2: Echovirus 18 capsid protein 2
L2: Echovirus 18 capsid protein 3
G2: Echovirus 18 capsid protein 1
H2: Echovirus 18 capsid protein 2
I2: Echovirus 18 capsid protein 3
D2: Echovirus 18 capsid protein 1
E2: Echovirus 18 capsid protein 2
F2: Echovirus 18 capsid protein 3
C2: Echovirus 18 capsid protein 3
B2: Echovirus 18 capsid protein 2


Theoretical massNumber of molelcules
Total (without water)2,187,76475
Polymers2,187,76475
Non-polymers00
Water0
1
A1: Echovirus 18 capsid protein 1
V1: Echovirus 18 capsid protein 1
W1: Echovirus 18 capsid protein 2
X1: Echovirus 18 capsid protein 3
S1: Echovirus 18 capsid protein 1
T1: Echovirus 18 capsid protein 2
U1: Echovirus 18 capsid protein 3
P1: Echovirus 18 capsid protein 1
Q1: Echovirus 18 capsid protein 2
R1: Echovirus 18 capsid protein 3
M1: Echovirus 18 capsid protein 1
N1: Echovirus 18 capsid protein 2
O1: Echovirus 18 capsid protein 3
J1: Echovirus 18 capsid protein 1
K1: Echovirus 18 capsid protein 2
L1: Echovirus 18 capsid protein 3
G1: Echovirus 18 capsid protein 1
H1: Echovirus 18 capsid protein 2
I1: Echovirus 18 capsid protein 3
D1: Echovirus 18 capsid protein 1
E1: Echovirus 18 capsid protein 2
F1: Echovirus 18 capsid protein 3
C1: Echovirus 18 capsid protein 3
B1: Echovirus 18 capsid protein 2
A2: Echovirus 18 capsid protein 1
w2: Echovirus 18 capsid protein 1
x2: Echovirus 18 capsid protein 2
y2: Echovirus 18 capsid protein 3
t2: Echovirus 18 capsid protein 1
u2: Echovirus 18 capsid protein 2
v2: Echovirus 18 capsid protein 3
q2: Echovirus 18 capsid protein 1
r2: Echovirus 18 capsid protein 2
s2: Echovirus 18 capsid protein 3
n2: Echovirus 18 capsid protein 1
o2: Echovirus 18 capsid protein 2
p2: Echovirus 18 capsid protein 3
k2: Echovirus 18 capsid protein 1
l2: Echovirus 18 capsid protein 2
m2: Echovirus 18 capsid protein 3
h2: Echovirus 18 capsid protein 1
i2: Echovirus 18 capsid protein 2
j2: Echovirus 18 capsid protein 3
e2: Echovirus 18 capsid protein 1
f2: Echovirus 18 capsid protein 2
g2: Echovirus 18 capsid protein 3
b2: Echovirus 18 capsid protein 1
c2: Echovirus 18 capsid protein 2
d2: Echovirus 18 capsid protein 3
Y2: Echovirus 18 capsid protein 1
Z2: Echovirus 18 capsid protein 2
a2: Echovirus 18 capsid protein 3
V2: Echovirus 18 capsid protein 1
W2: Echovirus 18 capsid protein 2
X2: Echovirus 18 capsid protein 3
S2: Echovirus 18 capsid protein 1
T2: Echovirus 18 capsid protein 2
U2: Echovirus 18 capsid protein 3
P2: Echovirus 18 capsid protein 1
Q2: Echovirus 18 capsid protein 2
R2: Echovirus 18 capsid protein 3
M2: Echovirus 18 capsid protein 1
N2: Echovirus 18 capsid protein 2
O2: Echovirus 18 capsid protein 3
J2: Echovirus 18 capsid protein 1
K2: Echovirus 18 capsid protein 2
L2: Echovirus 18 capsid protein 3
G2: Echovirus 18 capsid protein 1
H2: Echovirus 18 capsid protein 2
I2: Echovirus 18 capsid protein 3
D2: Echovirus 18 capsid protein 1
E2: Echovirus 18 capsid protein 2
F2: Echovirus 18 capsid protein 3
C2: Echovirus 18 capsid protein 3
B2: Echovirus 18 capsid protein 2

A1: Echovirus 18 capsid protein 1
V1: Echovirus 18 capsid protein 1
W1: Echovirus 18 capsid protein 2
X1: Echovirus 18 capsid protein 3
S1: Echovirus 18 capsid protein 1
T1: Echovirus 18 capsid protein 2
U1: Echovirus 18 capsid protein 3
P1: Echovirus 18 capsid protein 1
Q1: Echovirus 18 capsid protein 2
R1: Echovirus 18 capsid protein 3
M1: Echovirus 18 capsid protein 1
N1: Echovirus 18 capsid protein 2
O1: Echovirus 18 capsid protein 3
J1: Echovirus 18 capsid protein 1
K1: Echovirus 18 capsid protein 2
L1: Echovirus 18 capsid protein 3
G1: Echovirus 18 capsid protein 1
H1: Echovirus 18 capsid protein 2
I1: Echovirus 18 capsid protein 3
D1: Echovirus 18 capsid protein 1
E1: Echovirus 18 capsid protein 2
F1: Echovirus 18 capsid protein 3
C1: Echovirus 18 capsid protein 3
B1: Echovirus 18 capsid protein 2
A2: Echovirus 18 capsid protein 1
w2: Echovirus 18 capsid protein 1
x2: Echovirus 18 capsid protein 2
y2: Echovirus 18 capsid protein 3
t2: Echovirus 18 capsid protein 1
u2: Echovirus 18 capsid protein 2
v2: Echovirus 18 capsid protein 3
q2: Echovirus 18 capsid protein 1
r2: Echovirus 18 capsid protein 2
s2: Echovirus 18 capsid protein 3
n2: Echovirus 18 capsid protein 1
o2: Echovirus 18 capsid protein 2
p2: Echovirus 18 capsid protein 3
k2: Echovirus 18 capsid protein 1
l2: Echovirus 18 capsid protein 2
m2: Echovirus 18 capsid protein 3
h2: Echovirus 18 capsid protein 1
i2: Echovirus 18 capsid protein 2
j2: Echovirus 18 capsid protein 3
e2: Echovirus 18 capsid protein 1
f2: Echovirus 18 capsid protein 2
g2: Echovirus 18 capsid protein 3
b2: Echovirus 18 capsid protein 1
c2: Echovirus 18 capsid protein 2
d2: Echovirus 18 capsid protein 3
Y2: Echovirus 18 capsid protein 1
Z2: Echovirus 18 capsid protein 2
a2: Echovirus 18 capsid protein 3
V2: Echovirus 18 capsid protein 1
W2: Echovirus 18 capsid protein 2
X2: Echovirus 18 capsid protein 3
S2: Echovirus 18 capsid protein 1
T2: Echovirus 18 capsid protein 2
U2: Echovirus 18 capsid protein 3
P2: Echovirus 18 capsid protein 1
Q2: Echovirus 18 capsid protein 2
R2: Echovirus 18 capsid protein 3
M2: Echovirus 18 capsid protein 1
N2: Echovirus 18 capsid protein 2
O2: Echovirus 18 capsid protein 3
J2: Echovirus 18 capsid protein 1
K2: Echovirus 18 capsid protein 2
L2: Echovirus 18 capsid protein 3
G2: Echovirus 18 capsid protein 1
H2: Echovirus 18 capsid protein 2
I2: Echovirus 18 capsid protein 3
D2: Echovirus 18 capsid protein 1
E2: Echovirus 18 capsid protein 2
F2: Echovirus 18 capsid protein 3
C2: Echovirus 18 capsid protein 3
B2: Echovirus 18 capsid protein 2


Theoretical massNumber of molelcules
Total (without water)4,375,528150
Polymers4,375,528150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation1
Buried area509160 Å2
ΔGint-3071 kcal/mol
Surface area487090 Å2

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Components

#1: Protein ...
Echovirus 18 capsid protein 1


Mass: 32564.445 Da / Num. of mol.: 25 / 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: 28802.328 Da / Num. of mol.: 25 / 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: 26143.783 Da / Num. of mol.: 25 / 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: 6.77 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 chlorideNaClSodium chloride1
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 / 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
Image scansSampling size: 14 µm / Width: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1Gautomatch8particle selection
2EPUimage acquisition
4Gctf2.1CTF 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
Particle selectionNum. of particles selected: 509565
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7635 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 94.73 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factors / Details: Group B-factor refinement
Atomic model buildingPDB-ID: 6HBH

6hbh

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