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- PDB-3iyc: Poliovirus late RNA-release intermediate -

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Basic information

Entry
Database: PDB / ID: 3iyc
TitlePoliovirus late 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 / suppression by virus of host MDA-5 activity / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity ...caveolin-mediated endocytosis of virus by host cell / suppression by virus of host MDA-5 activity / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / suppression by virus of host RIG-I activity / picornain 3C / suppression by virus of host MAVS activity / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / pore formation by virus in membrane of host cell / integral to membrane of host cell / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / protein complex oligomerization / induction by virus of host autophagy / RNA-directed RNA polymerase / ion channel activity / suppression by virus of host gene expression / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / DNA replication / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding
picornavirus capsid protein / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Peptidase C3A/C3B, picornaviral / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase C3, picornavirus core protein 2A ...picornavirus capsid protein / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA-directed RNA polymerase, C-terminal domain / Peptidase C3A/C3B, picornaviral / Picornavirus capsid / Picornavirus 2B protein / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / Peptidase C3, picornavirus core protein 2A / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / Viral coat protein subunit / Poliovirus 3A protein-like / Picornavirus/Calicivirus coat protein
Genome polyprotein / Genome polyprotein / Genome polyprotein
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.
Validation Report
SummaryFull reportAbout validation report
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 1.2Nov 9, 2016Group: Other
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id

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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
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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
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
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
point symmetry operation5
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
point symmetry operation6
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

#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
#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 / Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: quantifoil holey grids 1.2/1.3
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 holderModel: 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
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms723 0 0 0 723

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