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

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Basic information

Entry
Database: PDB / ID: 5o5b
TitlePoliovirus type 3 (strain Saukett) stabilized virus-like particle
Components
  • Capsid proteins, VP1
  • Capsid proteins, VP2
  • Capsid proteins, VP3
  • Capsid proteins, VP4
KeywordsVIRUS LIKE PARTICLE / Poliovirus / virus-like particle / vaccine
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / 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 MDA-5 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...caveolin-mediated endocytosis of virus by host cell / 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 MDA-5 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 / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / : / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Jelly Rolls - #20 / 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) ...Jelly Rolls - #20 / 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 / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHuman poliovirus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 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 1, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id
Revision 1.2Aug 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 1.3Aug 30, 2017Group: Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.4Oct 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-3747
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  • Superimposition on EM map
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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


Theoretical massNumber of molelcules
Total (without water)97,5194
Polymers97,5194
Non-polymers00
Water0
1
1: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
x 60


Theoretical massNumber of molelcules
Total (without water)5,851,139240
Polymers5,851,139240
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: Capsid proteins, VP1
2: Capsid proteins, VP2
3: Capsid proteins, VP3
4: Capsid proteins, VP4
x 5


  • icosahedral pentamer
  • 488 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)487,59520
Polymers487,59520
Non-polymers00
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
x 6


  • icosahedral 23 hexamer
  • 585 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)585,11424
Polymers585,11424
Non-polymers00
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, UniProt: P03302*PLUS

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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: all / 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 / 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) were purified by Nycodenz gradients and assessed for monodispersity by negative stain EM analysis.
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 K / Details: Blot for 4 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: 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 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / 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) / Num. of grids imaged: 1 / Num. of real images: 2768
Image scansSampling size: 14 µm / 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 selectionNum. of particles selected: 37378
Details: Automated particle picking (ETHAN) was followed by manual cleaning (EMAN2).
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4046 / Algorithm: BACK PROJECTION / Num. of class averages: 3 / 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_d0.0096052
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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