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

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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 / homologyViral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A ...Viral coat protein subunit / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, catalytic domain / Picornavirus coat protein VP4 / Picornavirus 2B protein / Picornavirus capsid / RNA-directed RNA polymerase, C-terminal domain / Helicase, superfamily 3, single-stranded DNA/RNA virus / Peptidase C3A/C3B, picornaviral / Peptidase C3, picornavirus core protein 2A / Poliovirus core protein 3a, soluble domain / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded RNA virus / Poliovirus 3A protein-like / Peptidase S1, PA clan / RdRp of positive ssRNA viruses catalytic domain profile. / Picornavirus core protein 2A / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / P-loop containing nucleoside triphosphate hydrolase / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Picornavirus 2B protein / RNA helicase / RNA dependent RNA polymerase / caveolin-mediated endocytosis of virus by host cell / 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 / T=pseudo3 icosahedral viral capsid / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / RNA-directed RNA polymerase / suppression by virus of host gene expression / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / DNA replication / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceHuman poliovirus 1 Mahoney
Poliovirus type 3
Human poliovirus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 10 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2009 / Release: Mar 16, 2010
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 16, 2010Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jan 28, 2015Structure modelDatabase references
1.3Nov 9, 2016Structure modelOther
1.4Jul 18, 2018Structure modelData collectionem_image_scans / em_software_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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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
Polyers81,9915
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
Polyers4,919,464300
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
Polyers409,95525
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
Polyers491,94630
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

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Components

#1: Protein/peptide Genome polyprotein / 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: (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 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: (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/peptide Precursor polyprotein / Coordinate model: Cα atoms only


Mass: 25777.613 Da / Num. of mol.: 1 / Source: (gene. exp.) Human poliovirus 1 / References: UniProt: Q9E912, UniProt: P03300*PLUS
#4: Protein/peptide Genome polyprotein / 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: (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: (gene. exp.) Human poliovirus 1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / Virus host category: VERTEBRATES / Virus isolate: SEROTYPE / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl / Details: 20mM Tris pH 7.4, 2mM CaCl2, 20mM NaCl / pH: 7.4
SpecimenConc.: 0.2 / Details: 20mM Tris, 50mM NaCl, 2 mM CaCl2 / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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
MicroscopyMicroscope model: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal magnification: 59000 / Nominal defocus max: 3 / Nominal defocus min: 0.9 / Camera length: 0
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Specimen holder type: Eucentric / Tilt angle max: 0 / Tilt angle min: 0
Image recordingElectron dose: 15 / 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
3D reconstructionMethod: PFT / Resolution: 10 / 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 buildingDetails: REFINEMENT PROTOCOL--Rigid Body / Ref protocol: RIGID BODY FIT / Ref space: RECIPROCAL
Atomic model buildingPDB-ID: 1POV
Number of atoms included #LASTProtein: 723 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 723

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