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- PDB-5o5b: Poliovirus type 3 (strain Saukett) stabilized virus-like particle -

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Entry
Database: PDB / ID: 5o5b
TitlePoliovirus type 3 (strain Saukett) stabilized virus-like particle
Components
  • (Capsid proteinsCapsid) x 3
  • VP4
KeywordsVIRUS LIKE PARTICLE / Poliovirus / virus-like particle / vaccine
Function / homologyPicornavirus/Calicivirus coat protein / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan / 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 ...Picornavirus/Calicivirus coat protein / 3C cysteine protease (picornain 3C) / Peptidase S1, PA clan / 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 / picornavirus capsid protein / Poliovirus core protein 3a, soluble domain / Poliovirus 3A protein-like / P-loop containing nucleoside triphosphate hydrolase / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA dependent RNA polymerase / RdRp of positive ssRNA viruses catalytic domain profile. / RNA helicase / Picornavirus core protein 2A / Poliovirus 3A protein like / Picornavirus coat protein (VP4) / Viral coat protein subunit / Picornavirus 2B protein / 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 / suppression by virus of host RIG-I activity / T=pseudo3 icosahedral viral capsid / picornain 3C / 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 / 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 / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein / Capsid proteins
Function and homology information
Specimen sourceHuman poliovirus 3
Poliovirus type 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsBahar, M.W. / Kotecha, A. / Fry, E.E. / Stuart, D.I.
CitationJournal: Nat Commun / Year: 2017
Title: Plant-made polio type 3 stabilized VLPs-a candidate synthetic polio vaccine.
Authors: Johanna Marsian / Helen Fox / Mohammad W Bahar / Abhay Kotecha / Elizabeth E Fry / David I Stuart / Andrew J Macadam / David J Rowlands / George P Lomonossoff
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 1, 2017 / Release: Jul 12, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 12, 2017Structure modelrepositoryInitial release
1.1Jul 19, 2017Structure modelSource and taxonomyentity_src_gen_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
1.2Aug 23, 2017Structure modelDatabase referencescitation_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
1.3Aug 30, 2017Structure modelRefinement descriptionem_3d_fitting_em_3d_fitting.target_criteria

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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-3747
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  • Superimposition on EM map
  • EMDB-3747
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Capsid proteins
2: Capsid proteins
3: Capsid proteins
4: VP4


Theoretical massNumber of molelcules
Total (without water)97,5194
Polyers97,5194
Non-polymers00
Water0
1
1: Capsid proteins
2: Capsid proteins
3: Capsid proteins
4: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,851,139240
Polyers5,851,139240
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: Capsid proteins
2: Capsid proteins
3: Capsid proteins
4: VP4
x 5


  • icosahedral pentamer
  • 488 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)487,59520
Polyers487,59520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: Capsid proteins
2: Capsid proteins
3: Capsid proteins
4: VP4
x 6


  • icosahedral 23 hexamer
  • 585 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)585,11424
Polyers585,11424
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 Capsid proteins / Capsid


Mass: 33562.785 Da / Num. of mol.: 1 / Mutation: T105M, F132L / Source: (gene. exp.) Human poliovirus 3 / Plasmid name: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#2: Protein/peptide Capsid proteins / Capsid


Mass: 30188.982 Da / Num. of mol.: 1 / Mutation: L18I, L215M, D241E / Source: (gene. exp.) Human poliovirus 3 / Plasmid name: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#3: Protein/peptide Capsid proteins / Capsid


Mass: 26315.100 Da / Num. of mol.: 1 / Mutation: H19Y, L85F / Source: (gene. exp.) Human poliovirus 3 / Plasmid name: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#4: Protein/peptide VP4


Mass: 7452.113 Da / Num. of mol.: 1 / Mutation: T67A
Source: (gene. exp.) Poliovirus type 3 (strains P3/Leon/37 and P3/Leon 12A[1]B)
Strain: s P3/Leon/37 and P3/Leon 12A[1]B / Plasmid name: pEAQ-HT / Production host: Nicotiana benthamiana (plant)
References: UniProt: P03302, picornain 2A, nucleoside-triphosphate phosphatase, picornain 3C, RNA-directed RNA polymerase

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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: Human poliovirus 3 / Type: VIRUS
Details: Poliovirus type 3 (Saukett strain) virus-like particle produced in plant expression system.
Entity ID: 1, 2, 3, 4 / Source: RECOMBINANT
Molecular weightValue: 5.8 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 3
Source (recombinant)Organism: Nicotiana benthamiana (plant) / Plasmid: pEAQ-HT
Details of virusEmpty: YES / Enveloped: NO / Virus isolate: SEROTYPE / Virus type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Human poliovirus 3 / Strain: Saukett
Virus shellName: Capsid / Diameter: 327 nm / Triangulation number (T number): 1
Buffer solutionDetails: PBS pH 7.0 / pH: 7
SpecimenConc.: 0.1 mg/ml
Details: Virus-like particles for polio type 3 (strain Saukett) were purified by Nycodenz gradients and assessed for monodispersity by negative stain EM analysis.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat CF-2/1-2C
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 kelvins / Details: Blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 133333 / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 5 microns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2768
Image scansSampling size: 14 microns / Width: 4086 / Height: 4086 / Movie frames/image: 33 / Used frames/image: 2-33

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Processing

SoftwareName: PHENIX / Version: 1.12rc0_2787: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1ETHANparticle selection
2EPUimage acquisition
4RELION1.3CTF correctionCTFFIND3 module within RELION
7UCSF Chimera1.12model fitting
9PHENIX1.12rc0model refinement
10RELION1.3initial Euler assignment
11RELION1.3final Euler assignment
12RELION1.3classification
13RELION1.33D reconstruction
Image processingDetails: The selected images were drift corrected using MotionCorr.
CTF correctionDetails: CTF parameters were estimated using CTFFIND3 as part of RELION 1.3.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionDetails: Automated particle picking (ETHAN) was followed by manual cleaning (EMAN2).
Number of particles selected: 37378
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 4046 / Algorithm: BACK PROJECTION / Number of class averages: 3 / Symmetry type: POINT
Atomic model buildingDetails: phenix.real_space_refine was used to refine the atomic model in the cryo-em map.
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0096052
ELECTRON MICROSCOPYf_angle_d0.8698255
ELECTRON MICROSCOPYf_dihedral_angle_d9.5413600
ELECTRON MICROSCOPYf_chiral_restr0.056909
ELECTRON MICROSCOPYf_plane_restr0.0071067

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