|Entry||Database: EMDB / Id: 182|
|Title||Echovirus 18 A-particle|
|Map data||Echovirus 18 altered particle B-sharped map|
virus / (Echovirus 18 capsid protein ...) x 3
|Func homology||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 ...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
|Method||single particle reconstruction / cryo EM / Resolution: 3.36 Å|
|Authors||Buchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P|
|Citation||Journal: Nat Commun / Year: 2019|
Title: Enterovirus particles expel capsid pentamers to enable genome release.
P-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||PDB-ID: 6hbh|
SummaryFull reportAbout validation report
|Date||Deposition: Aug 10, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Mar 20, 2019 / Last update: Mar 20, 2019|
|Structure viewer||EM map: |
|File||emd_0182.map.gz (map file in CCP4 format, 171501 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.063 Å|
CCP4 map header:
-Entire Echovirus E18
|Entire||Name: Echovirus E18 / Number of components: 4|
-Component #1: virus, Echovirus E18
|Virus||Name: Echovirus E18 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN|
|Mass||Theoretical: 7.63 MDa|
|Species||Species: Echovirus E18 / Strain: Metcalf|
|Source (natural)||Host Species: Homo sapiens (human)|
|Shell #1||Name of element: Capsid / Diameter: 330.0 Å / T number(triangulation number): 1|
-Component #2: protein, Echovirus 18 capsid protein 1
|Protein||Name: Echovirus 18 capsid protein 1 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 32.564445 kDa|
|Source||Species: Echovirus E18|
-Component #3: protein, Echovirus 18 capsid protein 2
|Protein||Name: Echovirus 18 capsid protein 2 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 28.802328 kDa|
|Source||Species: Echovirus E18|
-Component #4: protein, Echovirus 18 capsid protein 3
|Protein||Name: Echovirus 18 capsid protein 3 / Number of Copies: 1 / Recombinant expression: No|
|Mass||Theoretical: 26.143783 kDa|
|Source||Species: Echovirus E18|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Specimen conc.: 3 mg/ml / Ph: 5.8|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 48 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 75000.0 X (nominal), 79725.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 3000.0 nm|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: FEI FALCON II (4k x 4k)|
|Image acquisition||Number of digital images: 2344 / Sampling size: 14 microns|
-Atomic model buiding
|Modeling #1||Refinement protocol: flexible / Target criteria: R-factors / Refinement space: RECIPROCAL|
Details: Reciprocal space refinement of atom positions and group B-factors
Overall bvalue: 163.98
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