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- PDB-6thn: Multiple Genomic RNA-Coat Protein Contacts Play Vital Roles in th... -

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Basic information

Entry
Database: PDB / ID: 6thn
TitleMultiple Genomic RNA-Coat Protein Contacts Play Vital Roles in the Assembly of Infectious Enterovirus-E symmetry expansion+2fold focused classification
Components
  • (Genome polyprotein) x 4
  • RNA Peak 9 Bernoulli Plot
KeywordsVIRUS / BEV1 / enterovirus / picornavirus / RNA
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 / ribonucleoside triphosphate phosphatase activity / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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
Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / 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 ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus coat protein / 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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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
MYRISTIC ACID / RNA / RNA (> 10) / Genome polyprotein
Similarity search - Component
Biological speciesBovine enterovirus
Bovine enterovirus strain VG-5-27
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsChandler-Bostock, R. / Mata, C.P. / Bingham, R. / Dykeman, E.J. / Meng, B. / Tuthill, T.J. / Rowlands, D.J. / Ranson, N.A. / Twarock, R. / Stockley, P.G.
Funding support United Kingdom, 7items
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 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-10506
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  • Superimposition on EM map
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Movie viewer
Structure viewerMolecule:
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Assembly

Deposited unit
1: Genome polyprotein
2: Genome polyprotein
3: Genome polyprotein
4: Genome polyprotein
A: RNA Peak 9 Bernoulli Plot
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0339
Polymers94,3845
Non-polymers6494
Water1,74797
1
1: Genome polyprotein
2: Genome polyprotein
3: Genome polyprotein
4: Genome polyprotein
A: RNA Peak 9 Bernoulli Plot
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,701,975540
Polymers5,663,043300
Non-polymers38,932240
Water3,243180
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: Genome polyprotein
2: Genome polyprotein
3: Genome polyprotein
4: Genome polyprotein
A: RNA Peak 9 Bernoulli Plot
hetero molecules
x 5


  • icosahedral pentamer
  • 475 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)475,16545
Polymers471,92025
Non-polymers3,24420
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Genome polyprotein
2: Genome polyprotein
3: Genome polyprotein
4: Genome polyprotein
A: RNA Peak 9 Bernoulli Plot
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 570 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)570,19754
Polymers566,30430
Non-polymers3,89324
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

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Protein , 4 types, 4 molecules 1234

#1: Protein Genome polyprotein


Mass: 31280.955 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine enterovirus (strain VG-5-27)
References: UniProt: P12915, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein Genome polyprotein


Mass: 27325.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine enterovirus (strain VG-5-27)
References: UniProt: P12915, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Genome polyprotein


Mass: 26627.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine enterovirus (strain VG-5-27)
References: UniProt: P12915, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#4: Protein Genome polyprotein


Mass: 5619.105 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine enterovirus (strain VG-5-27)
References: UniProt: P12915, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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RNA chain , 1 types, 1 molecules A

#5: RNA chain RNA Peak 9 Bernoulli Plot


Mass: 3531.162 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bovine enterovirus strain VG-5-27

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Non-polymers , 3 types, 101 molecules

#6: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: Bovine enterovirus strain VG-5-27 / Type: VIRUS / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Bovine enterovirus strain VG-5-27
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Virus shellTriangulation number (T number): 3
Buffer solutionpH: 7.4 / Details: PBS
Buffer componentFormula: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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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: OTHER / Nominal magnification: 75000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 49.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of real images: 8785

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
13Coot0.9model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 260348
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 946982 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingSpace: REAL
Atomic model buildingPDB-ID: 1BEV

1bev


Accession code: 1BEV / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01391740
ELECTRON MICROSCOPYf_angle_d1.006534060
ELECTRON MICROSCOPYf_dihedral_angle_d4.503231600
ELECTRON MICROSCOPYf_chiral_restr0.06558860
ELECTRON MICROSCOPYf_plane_restr0.00769240

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