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- PDB-5o5p: Poliovirus type 3 (strain Saukett) stabilized virus-like particle... -

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Basic information

Entry
Database: PDB / ID: 5o5p
TitlePoliovirus type 3 (strain Saukett) stabilized virus-like particle in complex with the pocket factor compound GPP3
Components
  • Capsid proteins, VP1
  • Capsid proteins, VP2
  • Capsid proteins, VP3
  • Capsid proteins, VP4
KeywordsVIRUS LIKE PARTICLE / Poliovirus / virus-like particle / vaccine / pocket factor
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / symbiont-mediated suppression of host gene expression / structural molecule activity / virion attachment to host cell
Similarity search - Function
Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Chem-9LW / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBahar, M.W. / Kotecha, A. / Fry, E.E. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
WHO/Gates foundationRG.IMCB.I8-TSA-083 United Kingdom
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 /
Abstract: Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust ...Poliovirus (PV) is the causative agent of poliomyelitis, a crippling human disease known since antiquity. PV occurs in two distinct antigenic forms, D and C, of which only the D form elicits a robust neutralizing response. Developing a synthetically produced stabilized virus-like particle (sVLP)-based vaccine with D antigenicity, without the drawbacks of current vaccines, will be a major step towards the final eradication of poliovirus. Such a sVLP would retain the native antigenic conformation and the repetitive structure of the original virus particle, but lack infectious genomic material. In this study, we report the production of synthetically stabilized PV VLPs in plants. Mice carrying the gene for the human PV receptor are protected from wild-type PV when immunized with the plant-made PV sVLPs. Structural analysis of the stabilized mutant at 3.6 Å resolution by cryo-electron microscopy and single-particle reconstruction reveals a structure almost indistinguishable from wild-type PV3.Despite the success of current vaccination against poliomyelitis, safe, cheap and effective vaccines remain sought for continuing eradication effort. Here the authors use plants to express stabilized virus-like particles of type 3 poliovirus that can induce a protective immune response in mice transgenic for the human poliovirus receptor.
History
DepositionJun 2, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
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
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_imaging_optics
Item: _em_3d_fitting.target_criteria / _em_imaging_optics.energyfilter_name
Revision 1.3Oct 2, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 2.0Sep 21, 2022Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / entity_src_gen / pdbx_struct_oper_list / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession

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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-3749
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  • Superimposition on EM map
  • EMDB-3749
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Structure viewerMolecule:
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Assembly

Deposited unit
1: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,9275
Polymers97,5194
Non-polymers4081
Water0
1
1: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,875,648300
Polymers5,851,139240
Non-polymers24,51060
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
Buried area14260 Å2
ΔGint-79 kcal/mol
Surface area34690 Å2
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
1: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 490 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)489,63725
Polymers487,59520
Non-polymers2,0425
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 588 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)587,56530
Polymers585,11424
Non-polymers2,4516
Water0
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

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Components

#1: Protein Capsid proteins, VP1 /


Mass: 33562.785 Da / Num. of mol.: 1 / Mutation: T105M, F132L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#2: Protein Capsid proteins, VP2 /


Mass: 30188.982 Da / Num. of mol.: 1 / Mutation: L18I, L215M, D241E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#3: Protein Capsid proteins, VP3 /


Mass: 26315.100 Da / Num. of mol.: 1 / Mutation: H19Y, L85F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#4: Protein Capsid proteins, VP4 /


Mass: 7452.113 Da / Num. of mol.: 1 / Mutation: T67A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human poliovirus 3 / Strain: Saukett / Plasmid: pEAQ-HT / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q84895
#5: Chemical ChemComp-9LW / 1-[5-[4-(ethoxyiminomethyl)phenoxy]-3-methyl-pentyl]-3-pyridin-4-yl-imidazol-2-one


Mass: 408.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28N4O3

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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: Human poliovirus 3 / Type: VIRUS
Details: Poliovirus type 3 (Saukett strain) virus-like particle produced in plant expression system.
Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightValue: 5.8 MDa / Experimental value: NO
Source (natural)Organism: Human poliovirus 3 / Strain: Saukett
Source (recombinant)Organism: Nicotiana benthamiana (plant) / Plasmid: pEAQ-HT
Details of virusEmpty: YES / Enveloped: NO / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Human poliovirus 3 / Strain: Saukett
Virus shellName: Capsid / Diameter: 327 nm / Triangulation number (T number): 1
Buffer solutionpH: 7 / Details: PBS pH 7.0
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Virus-like particles for polio type 3 (strain Saukett) in complex with pocket factor compound GPP3 were assessed by negative stain EM analysis, prior to cryo-em data collection.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat CF-2/1-2C
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 293 K / Details: Blot for 4 seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300 / Details: Preliminary grid screening was performed.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 37037 X / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 910 MULTI-SPECIMEN SINGLE TILT CRYO TRANSFER HOLDER
Image recordingAverage exposure time: 0.2 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1018
EM imaging opticsEnergyfilter name: GIF Quantum / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 5 µm / Width: 4086 / Height: 4086 / Movie frames/image: 25 / Used frames/image: 2-25

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Processing

SoftwareName: PHENIX / Version: 1.12rc0_2787: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1ETHAN1.2particle selection
2SerialEMimage acquisition
4RELION1.3CTF correctionCTFFIND3 module within RELION
7UCSF Chimera1.12model fitting
9RELION1.3initial Euler assignment
10RELION1.3final Euler assignment
11RELION1.3classification
12RELION1.33D reconstruction
13PHENIX1.12rc0model refinement
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 selectionNum. of particles selected: 6639
Details: Automated particle picking (ETHAN) was followed by manual cleaning (EMAN2).
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2060 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: phenix.real_space_refine was used to refine the atomic model in the cryo-em map.
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0066084
ELECTRON MICROSCOPYf_angle_d0.7858296
ELECTRON MICROSCOPYf_dihedral_angle_d9.413604
ELECTRON MICROSCOPYf_chiral_restr0.053909
ELECTRON MICROSCOPYf_plane_restr0.0071069

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