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Yorodumi- EMDB-10506: Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in th... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10506 | ||||||||||||||||||||||||
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Title | Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification | ||||||||||||||||||||||||
Map data | None | ||||||||||||||||||||||||
Sample |
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Keywords | BEV1 / enterovirus / picornavirus / RNA / VIRUS | ||||||||||||||||||||||||
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 / ribonucleoside triphosphate phosphatase activity / 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 / nucleoside-triphosphate phosphatase ...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 / ribonucleoside triphosphate phosphatase activity / 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 / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||||||||||||||
Biological species | Bovine enterovirus (strain VG-5-27) / Bovine enterovirus strain VG-5-27 | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | ||||||||||||||||||||||||
Authors | Chandler-Bostock R / Mata CP / Bingham R / Dykeman EC / Meng B / Tuthill TJ / Rowlands DJ / Ranson NA / Twarock R / Stockley PG | ||||||||||||||||||||||||
Funding support | United Kingdom, 7 items
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Citation | Journal: PLoS Pathog / Year: 2020 Title: Assembly of infectious enteroviruses depends on multiple, conserved genomic RNA-coat protein contacts. Authors: Rebecca Chandler-Bostock / Carlos P Mata / Richard J Bingham / Eric C Dykeman / Bo Meng / Tobias J Tuthill / David J Rowlands / Neil A Ranson / Reidun Twarock / Peter G Stockley / Abstract: Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral ...Picornaviruses are important viral pathogens, but despite extensive study, the assembly process of their infectious virions is still incompletely understood, preventing the development of anti-viral strategies targeting this essential part of the life cycle. We report the identification, via RNA SELEX and bioinformatics, of multiple RNA sites across the genome of a typical enterovirus, enterovirus-E (EV-E), that each have affinity for the cognate viral capsid protein (CP) capsomer. Many of these sites are evolutionarily conserved across known EV-E variants, suggesting they play essential functional roles. Cryo-electron microscopy was used to reconstruct the EV-E particle at ~2.2 Å resolution, revealing extensive density for the genomic RNA. Relaxing the imposed symmetry within the reconstructed particles reveals multiple RNA-CP contacts, a first for any picornavirus. Conservative mutagenesis of the individual RNA-contacting amino acid side chains in EV-E, many of which are conserved across the enterovirus family including poliovirus, is lethal but does not interfere with replication or translation. Anti-EV-E and anti-poliovirus aptamers share sequence similarities with sites distributed across the poliovirus genome. These data are consistent with the hypothesis that these RNA-CP contacts are RNA Packaging Signals (PSs) that play vital roles in assembly and suggest that the RNA PSs are evolutionarily conserved between pathogens within the family, augmenting the current protein-only assembly paradigm for this family of viruses. | ||||||||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10506.map.gz | 223.4 MB | EMDB map data format | |
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Header (meta data) | emd-10506-v30.xml emd-10506.xml | 18.8 KB 18.8 KB | Display Display | EMDB header |
Images | emd_10506.png | 264.3 KB | ||
Filedesc metadata | emd-10506.cif.gz | 6.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10506 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10506 | HTTPS FTP |
-Validation report
Summary document | emd_10506_validation.pdf.gz | 190.4 KB | Display | EMDB validaton report |
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Full document | emd_10506_full_validation.pdf.gz | 189.9 KB | Display | |
Data in XML | emd_10506_validation.xml.gz | 502 B | Display | |
Data in CIF | emd_10506_validation.cif.gz | 374 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10506 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10506 | HTTPS FTP |
-Related structure data
Related structure data | 6thnMC 6thdC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10506.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Bovine enterovirus strain VG-5-27
Entire | Name: Bovine enterovirus strain VG-5-27 |
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Components |
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-Supramolecule #1: Bovine enterovirus strain VG-5-27
Supramolecule | Name: Bovine enterovirus strain VG-5-27 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / NCBI-ID: 12065 / Sci species name: Bovine enterovirus strain VG-5-27 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Virus shell | Shell ID: 1 / T number (triangulation number): 3 |
-Macromolecule #1: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Bovine enterovirus (strain VG-5-27) |
Molecular weight | Theoretical: 31.280955 KDa |
Sequence | String: NDPGKMLKDA IDKQVAGALV AGTTTSTHSV ATDSTPALQA AETGATSTAR DESMIETRTI VPTHGIHETS VESFFGRSSL VGMPLLATG TSITHWRIDF REFVQLRAKM SWFTYMRFDV EFTIIATSST GQNVTTEQHT TYQVMYVPPG APVPSNQDSF Q WQSGCNPS ...String: NDPGKMLKDA IDKQVAGALV AGTTTSTHSV ATDSTPALQA AETGATSTAR DESMIETRTI VPTHGIHETS VESFFGRSSL VGMPLLATG TSITHWRIDF REFVQLRAKM SWFTYMRFDV EFTIIATSST GQNVTTEQHT TYQVMYVPPG APVPSNQDSF Q WQSGCNPS VFADTDGPPA QFSVPFMSSA NAYSTVYDGY ARFMDTDPDR YGILPSNFLG FMYFRTLEDA AHQVRFRIYA KI KHTSCWI PRAPRQAPYK KRYNLVFSGD SDRICSNRAS LTSY UniProtKB: Genome polyprotein |
-Macromolecule #2: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Bovine enterovirus (strain VG-5-27) |
Molecular weight | Theoretical: 27.325604 KDa |
Sequence | String: SPSAEACGYS DRVAQLTLGN STITTQEAAN ICVAYGCWPA KLSDTDATSV DKPTEPGVSA DRFYTLRSKP WQADSKGWYW KLPDALNNT GMFGQNAQFH YIYRGGWAVH VQCNATKFHQ GTLLVLAIPE HQIATQEQPA FDRTMPGSEG GTFQEPFWLE D GTSLGNSL ...String: SPSAEACGYS DRVAQLTLGN STITTQEAAN ICVAYGCWPA KLSDTDATSV DKPTEPGVSA DRFYTLRSKP WQADSKGWYW KLPDALNNT GMFGQNAQFH YIYRGGWAVH VQCNATKFHQ GTLLVLAIPE HQIATQEQPA FDRTMPGSEG GTFQEPFWLE D GTSLGNSL IYPHQWINLR TNNSATLILP YVNAIPMDSA IRHSNWTLAI IPVAPLKYAA ETTPLVPITV TIAPMETEYN GL RRAIASN Q UniProtKB: Genome polyprotein |
-Macromolecule #3: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Bovine enterovirus (strain VG-5-27) |
Molecular weight | Theoretical: 26.627221 KDa |
Sequence | String: GLPTKPGPGS YQFMTTDEDC SPCILPDFQP TPEIFIPGKV NNLLEIAQVE SILEANNREG VEGVERYVIP VSVQDALDAQ IYALRLELG GSGPLSSSLL GTLAKHYTQW SGSVEITCMF TGTFMTTGKV LLAYTPPGGD MPRNREEAML GTHVIWDFGL Q SSITLVIP ...String: GLPTKPGPGS YQFMTTDEDC SPCILPDFQP TPEIFIPGKV NNLLEIAQVE SILEANNREG VEGVERYVIP VSVQDALDAQ IYALRLELG GSGPLSSSLL GTLAKHYTQW SGSVEITCMF TGTFMTTGKV LLAYTPPGGD MPRNREEAML GTHVIWDFGL Q SSITLVIP WISASHFRGV SNDDVLNYQY YAAGHVTIWY QTNMVIPPGF PNTAGIIMMI AAQPNFSFRI QKDREDMTQT AI LQ UniProtKB: Genome polyprotein |
-Macromolecule #4: Genome polyprotein
Macromolecule | Name: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A |
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Source (natural) | Organism: Bovine enterovirus (strain VG-5-27) |
Molecular weight | Theoretical: 5.619105 KDa |
Sequence | String: GAQGGSTINY NNINYYSHAA SAAQNKQDFT QDPSKFTQPI ADVIKETAVP LK UniProtKB: Genome polyprotein |
-Macromolecule #5: RNA Peak 9 Bernoulli Plot
Macromolecule | Name: RNA Peak 9 Bernoulli Plot / type: rna / ID: 5 / Number of copies: 1 |
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Source (natural) | Organism: Bovine enterovirus strain VG-5-27 |
Molecular weight | Theoretical: 3.531162 KDa |
Sequence | String: AGAGCAUGAU U |
-Macromolecule #6: MYRISTIC ACID
Macromolecule | Name: MYRISTIC ACID / type: ligand / ID: 6 / Number of copies: 2 / Formula: MYR |
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Molecular weight | Theoretical: 228.371 Da |
Chemical component information | ChemComp-MYR: |
-Macromolecule #7: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: SO4 |
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Molecular weight | Theoretical: 96.063 Da |
Chemical component information | ChemComp-SO4: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 97 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Formula: PBS / Details: PBS |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 8785 / Average exposure time: 1.0 sec. / Average electron dose: 49.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 75000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |