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- PDB-3iyb: Poliovirus early RNA-release intermediate -

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Basic information

Entry
Database: PDB / ID: 3iyb
TitlePoliovirus early RNA-release intermediate
Components
  • (Genome polyprotein) x 3
  • Precursor polyprotein
  • VP1 core
KeywordsVIRAL PROTEIN / Picornavirus / poliovirus / intermediate / RNA release / 80S / ATP-binding / Capsid protein / Covalent protein-RNA linkage / Cytoplasmic vesicle / Helicase / Host-virus interaction / Hydrolase / Lipoprotein / Membrane / Myristate / Nucleotide-binding / Nucleotidyltransferase / Phosphoprotein / Protease / RNA replication / RNA-binding / RNA-directed RNA polymerase / Thiol protease / Transferase / Virion
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host translation initiation / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host translation initiation / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / 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 / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
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 ...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
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 1 Mahoney
Poliovirus type 3
Human poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å
AuthorsLevy, H.C. / Bostina, M. / Filman, D.J. / Hogle, J.M.
CitationJournal: J Virol / Year: 2010
Title: Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy.
Authors: Hazel C Levy / Mihnea Bostina / David J Filman / James M Hogle /
Abstract: Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes ...Poliovirus infection requires that the particle undergo a series of conformational transitions that lead to cell entry and genome release. In an effort to understand the conformational changes associated with the release of the RNA genome, we have used cryo-electron microscopy to characterize the structure of the 80S "empty" particles of poliovirus that are thought to represent the final product of the cell entry pathway. Using two-dimensional classification methods, we show that preparations of 80S particles contain at least two structures, which might represent snapshots from a continuous series of conformers. Using three-dimensional reconstruction methods, we have solved the structure of two distinct forms at subnanometric resolution, and we have built and refined pseudoatomic models into the reconstructions. The reconstructions and the derived models demonstrate that the two structural forms are both slightly expanded, resulting in partial disruption of interprotomer interfaces near their particle 2-fold axes, which may represent the site where RNA is released. The models demonstrate that each of the two 80S structures has undergone a unique set of movements of the capsid proteins, associated with rearrangement of flexible loops and amino-terminal extensions that participate in contacts between protomers, between pentamers, and with the viral RNA.
History
DepositionJul 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Nov 9, 2016Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 21, 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-5123
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Genome polyprotein
2: Genome polyprotein
3: Precursor polyprotein
4: Genome polyprotein
7: VP1 core


Theoretical massNumber of molelcules
Total (without water)81,9915
Polymers81,9915
Non-polymers00
Water0
1
1: Genome polyprotein
2: Genome polyprotein
3: Precursor polyprotein
4: Genome polyprotein
7: VP1 core
x 60


Theoretical massNumber of molelcules
Total (without water)4,919,464300
Polymers4,919,464300
Non-polymers00
Water0
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: Precursor polyprotein
4: Genome polyprotein
7: VP1 core
x 5


  • icosahedral pentamer
  • 410 kDa, 25 polymers
Theoretical massNumber of molelcules
Total (without water)409,95525
Polymers409,95525
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Genome polyprotein
2: Genome polyprotein
3: Precursor polyprotein
4: Genome polyprotein
7: VP1 core
x 6


  • icosahedral 23 hexamer
  • 492 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)491,94630
Polymers491,94630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Genome polyprotein / Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B ...Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B / Protein VP3 / Virion protein 3 / P1C / Protein VP1 / Virion protein 1 / P1D / Picornain 2A / Protein 2A / P2A / Protein 2B / P2B / Protein 2C / P2C / Protein 3A / P3A / Protein 3B / P3B / VPg / Picornain 3C / Protease 3C / P3C / RNA-directed RNA polymerase 3D-POL / P3D-POL / Coordinate model: Cα atoms only


Mass: 26558.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney
References: UniProt: P03300, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#2: Protein/peptide Genome polyprotein / Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B ...Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B / Protein VP3 / Virion protein 3 / P1C / Protein VP1 / Virion protein 1 / P1D / Picornain 2A / Protein 2A / P2A / Protein 2B / P2B / Protein 2C / P2C / Protein 3A / P3A / Protein 3B / P3B / VPg / Picornain 3C / Protease 3C / P3C / RNA-directed RNA polymerase 3D-POL / P3D-POL / Coordinate model: Cα atoms only


Mass: 1518.665 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Poliovirus type 3 (strains P3/LEON/37 AND P3/LEON 12A[1]B)
References: UniProt: P03302, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#3: Protein Precursor polyprotein / Coordinate model: Cα atoms only


Mass: 25777.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 / References: UniProt: Q9E912, UniProt: P03300*PLUS
#4: Protein Genome polyprotein / Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B ...Protein VP0 / VP4-VP2 / Protein VP4 / Virion protein 4 / P1A / Protein VP2 / Virion protein 2 / P1B / Protein VP3 / Virion protein 3 / P1C / Protein VP1 / Virion protein 1 / P1D / Picornain 2A / Protein 2A / P2A / Protein 2B / P2B / Protein 2C / P2C / Protein 3A / P3A / Protein 3B / P3B / VPg / Picornain 3C / Protease 3C / P3C / RNA-directed RNA polymerase 3D-POL / P3D-POL / Coordinate model: Cα atoms only


Mass: 27181.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1 Mahoney
References: UniProt: P03300, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase
#5: Protein/peptide VP1 core / Coordinate model: Cα atoms only


Mass: 954.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 1

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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: 80S poliovirus / Type: VIRUS
Details: 60 promoters arranged as a icosahedron. native virus heat-treated at 56 degrees C
Synonym: poliovirus 1 mahoney
Molecular weightValue: 8.3 MDa / Experimental value: YES
Details of virusEmpty: YES / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl / pH: 7.4 / Details: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: blot for 3 secs

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 59000 X / Nominal defocus max: 3 nm / Nominal defocus min: 0.9 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategoryDetails
1INSOUTmodel fittingrigid body
2EM3DR23D reconstruction
3PFT23D reconstruction
CTF correctionDetails: each micrograph
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PFT / Resolution: 10 Å / Resolution method: FSC 0.5 CUT-OFF
Details: Details about the particle: 10,000 particle were partitioned into two distinct classes
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--Rigid Body
Atomic model buildingPDB-ID: 1POV
Accession code: 1POV / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 0 0 723

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