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- EMDB-0188: Echovirus 18 Open particle without three pentamers -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-0188
TitleEchovirus 18 Open particle without three pentamers
Map dataEchovirus 18 Open particle without three pentamers
Sample
  • Virus: Echovirus E18
    • Protein or peptide: Echovirus 18 capsid protein 1
    • Protein or peptide: Echovirus 18 capsid protein 2
    • Protein or peptide: Echovirus 18 capsid protein 3
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 / RNA helicase activity / DNA replication / 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 / host cell nucleus / 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 / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesEchovirus E18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsBuchta D / Fuzik T / Hrebik D / Levdansky Y / Moravcova J / Plevka P
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, 2018-
Header (metadata) releaseSep 12, 2018-
Map releaseMar 20, 2019-
UpdateMar 27, 2019-
Current statusMar 27, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hbl
  • Surface level: 0.066
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hbl
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0188.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEchovirus 18 Open particle without three pentamers
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 0.066 / Movie #1: 0.066
Minimum - Maximum-0.28856438 - 0.56822634
Average (Standard dev.)0.0014509568 (±0.0164822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 543.232 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z543.232543.232543.232
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-0.2890.5680.001

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Supplemental data

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Mask #1

Fileemd_0188_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Mask #2

Fileemd_0188_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Echovirus E18

EntireName: Echovirus E18
Components
  • Virus: Echovirus E18
    • Protein or peptide: Echovirus 18 capsid protein 1
    • Protein or peptide: Echovirus 18 capsid protein 2
    • Protein or peptide: Echovirus 18 capsid protein 3

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Supramolecule #1: Echovirus E18

SupramoleculeName: Echovirus E18 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 47506 / Sci species name: Echovirus E18 / Sci species strain: Metcalf / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.33 MDa
Virus shellShell ID: 1 / Name: Capsid / Diameter: 340.0 Å / T number (triangulation number): 1

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Macromolecule #1: Echovirus 18 capsid protein 1

MacromoleculeName: Echovirus 18 capsid protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 32.564445 KDa
SequenceString: GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT ...String:
GDNQDRTVAN TQPSGPSNST EIPALTAVET GHTSQVDPSD TIQTRHVVNF HSRSESTIEN FMGRAACVFM DQYKINGEET STDRFAVWT INIREMAQLR RKCEMFTYMR FDIEMTMVIT SCQDQGTILD QDMPVLTHQI MYVPPGGPIP AKVDGYEWQT S TNPSVFWT EGNAPPRISI PFISVGNAYS SFYDGWSHFT QDGTYGYTTL NAMGKLYIRH VNRSSPHQIT STIRVYFKPK HI KAWVPRP PRLCPYINKR DVNFVVTEIT DSRTSITDTP HPEHSVLATH

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Macromolecule #2: Echovirus 18 capsid protein 2

MacromoleculeName: Echovirus 18 capsid protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 28.802328 KDa
SequenceString: SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA ...String:
SPSAEECGYS DRVRSMTLGN STITTQESAN VVVGYGEWPS YLSDREATAE DQPTQPDVAT CRFYTLESVQ WEKTSPGWWW KFPEALKNM GLFGQNMHYH YLGRAGYTIH VQCNASKFHQ GCLLVVCVPE AEMGCADTDT TFPATELTTE DTPHVFTSDS I TGKKVQAA VCNAGMGVGV GNLTIFPHQW INLRTNNSAT IVIPYINSVP MDNMFRHYNF TLMIIPFAPL NFTDGATAYV PI TVTIAPM YAEYNGLRLA STQ

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Macromolecule #3: Echovirus 18 capsid protein 3

MacromoleculeName: Echovirus 18 capsid protein 3 / type: protein_or_peptide / ID: 3 / Number of copies: 15 / Enantiomer: LEVO
Source (natural)Organism: Echovirus E18
Molecular weightTheoretical: 26.143783 KDa
SequenceString: GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC ...String:
GVPVLNTPGS NQFLTSDDYQ SPSAMPQFDE TPEMHIPGEV RNLMEIAEVD SVVPVNNVTG KTKSMDAYQI PVGTGNTDKT KPIFSFQMD PGYSSVLKRT LLGEMLNYYA HWSGSVKLTF LFCGSAMATG KLLISYSPPG ASVPTSRKDA MLGTHIVWDI G LQSSCVLC VPWISQSHYR MVQQDPYTSA GYITCWYQTN IVVPPGAPTS CDVLCFASAC NDFSVRLLRD TPFMAQPGKL Q

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 6
Component:
ConcentrationFormulaName
37.5 mMMES2-(N-Morpholino)ethanesulfonic acid
5.0 mMTris2-Amino-2-(hydroxymethyl)-1,3-propanediol
25.0 mMNaClSodium chloridesodium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: FORMVAR / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.282 µm / Calibrated defocus min: 0.651 µm / Calibrated magnification: 79575 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Number real images: 6331 / Average exposure time: 1.0 sec. / Average electron dose: 45.2 e/Å2
Details: Images were collected in movie-mode at 39 frames per second
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

Details: Echovirus 18 A-particle
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 7791 / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 13635
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Overall B value: 92.45 / Target criteria: R-factor
Output model

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

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