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- EMDB-10504: Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in th... -

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Basic information

Entry
Database: EMDB / ID: EMD-10504
TitleMultiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E
Map dataBEV1 I2 cryoEM map at 2.23A resolution
Sample
  • Virus: Bovine enterovirus (strain VG-5-27)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: MYRISTIC ACID
  • Ligand: SULFATE IONSulfate
  • Ligand: water
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 / : ...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 / 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 / host cell nucleus / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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) ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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. / 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 speciesBovine enterovirus (strain VG-5-27)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.23 Å
AuthorsChandler-Bostock R / Mata CP / Bingham R / Dykeman EJ / Meng B / Tuthill TJ / Rowlands DJ / Ranson NA / Twarock R / Stockley PG
Funding support United Kingdom, 7 items
OrganizationGrant numberCountry
Wellcome Trust110145 United Kingdom
Wellcome Trust110146 United Kingdom
Wellcome Trust089311/Z/09/Z United Kingdom
Wellcome Trust090932/Z/09/Z United Kingdom
Wellcome Trust106692 United Kingdom
Royal SocietyLT130088 United Kingdom
Royal SocietyRSWF/R1/180009 United Kingdom
CitationJournal: 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
DepositionNov 19, 2019-
Header (metadata) releaseDec 9, 2020-
Map releaseDec 9, 2020-
UpdateJun 23, 2021-
Current statusJun 23, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.08
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  • Surface view with fitted model
  • Atomic models: PDB-6thd
  • Surface level: 0.08
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6thd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10504.png

Downloads & links

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Map

FileDownload / File: emd_10504.map.gz / Format: CCP4 / Size: 391 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBEV1 I2 cryoEM map at 2.23A resolution
Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.36726612 - 0.5326416
Average (Standard dev.)7.2316925e-06 (±0.029814651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-234-234-234
Dimensions468468468
Spacing468468468
CellA=B=C: 498.42 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z468468468
origin x/y/z0.0000.0000.000
length x/y/z498.420498.420498.420
α/β/γ90.00090.00090.000
start NX/NY/NZ-31-35-52
NX/NY/NZ11798209
MAP C/R/S123
start NC/NR/NS-234-234-234
NC/NR/NS468468468
D min/max/mean-0.3670.5330.000

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Supplemental data

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Sample components

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Entire : Bovine enterovirus (strain VG-5-27)

EntireName: Bovine enterovirus (strain VG-5-27)
Components
  • Virus: Bovine enterovirus (strain VG-5-27)
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
    • Protein or peptide: Genome polyprotein
  • Ligand: MYRISTIC ACID
  • Ligand: SULFATE IONSulfate
  • Ligand: water

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Supramolecule #1: Bovine enterovirus (strain VG-5-27)

SupramoleculeName: Bovine enterovirus (strain VG-5-27) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 12065 / Sci species name: Bovine enterovirus (strain VG-5-27) / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / T number (triangulation number): 3

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Macromolecule #1: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Bovine enterovirus (strain VG-5-27)
Molecular weightTheoretical: 31.280955 KDa
SequenceString: 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

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Macromolecule #2: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Bovine enterovirus (strain VG-5-27)
Molecular weightTheoretical: 27.325604 KDa
SequenceString: 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

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Macromolecule #3: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Bovine enterovirus (strain VG-5-27)
Molecular weightTheoretical: 26.627221 KDa
SequenceString: 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

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Macromolecule #4: Genome polyprotein

MacromoleculeName: Genome polyprotein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Bovine enterovirus (strain VG-5-27)
Molecular weightTheoretical: 5.619105 KDa
SequenceString:
GAQGGSTINY NNINYYSHAA SAAQNKQDFT QDPSKFTQPI ADVIKETAVP LK

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Macromolecule #5: MYRISTIC ACID

MacromoleculeName: MYRISTIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: MYR
Molecular weightTheoretical: 228.371 Da
Chemical component information

ChemComp-MYR:
MYRISTIC ACID / Myristic acid

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Macromolecule #6: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 97 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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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

BufferpH: 7.4 / Component - Formula: PBS / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 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 / Number real images: 8785 / Average exposure time: 1.0 sec. / Average electron dose: 49.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 260348
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.23 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 105723

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Atomic model buiding 1

Initial modelPDB ID:

1bev

RefinementSpace: REAL
Output model

PDB-6thd:
Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E

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