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

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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 / 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: 4.05 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 29, 2018 / Release: Mar 20, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 20, 2019Structure modelrepositoryInitial release
1.1Apr 10, 2019Structure modelData collection / Structure summaryem_admin / pdbx_database_proc / struct_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
Polyers2,187,76475
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
Polyers4,375,528150
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation1
Buried area (Å2)509160
ΔGint (kcal/M)-3071
Surface area (Å2)487090

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Components

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


Mass: 32564.445 Da / Num. of mol.: 25 / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635
#2: Protein/peptide ...
Echovirus 18 capsid protein 2


Mass: 28802.328 Da / Num. of mol.: 25 / Source: (natural) Echovirus E18 / Cell line: GMK / References: UniProt: Q8V635
#3: Protein/peptide ...
Echovirus 18 capsid protein 3


Mass: 26143.783 Da / Num. of mol.: 25 / 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: 1, 2, 3 / Source: NATURAL
Molecular weightValue: 6.77 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: 340 nm / Triangulation number (T number): 1
Buffer solutionpH: 6
Buffer component

Buffer-ID: 1

IDConc. (mg/ml)NameFormula
137.5 mM2-(N-Morpholino)ethanesulfonic acidMES
25 mM2-Amino-2-(hydroxymethyl)-1,3-propanediolTris
325 mMsodium chlorideNaCl
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 / 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: 79575 / 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 microns / 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
Image scansSampling size: 14 microns / 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 buildingDetails: Group B-factor refinement / B value: 94.73 / Protocol: RIGID BODY FIT / Space: RECIPROCAL / Target criteria: R-factors
Atomic model buildingPDB-ID: 6HBH

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