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- EMDB-50189: Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (... -

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Basic information

Entry
Database: EMDB / ID: EMD-50189
TitlePoliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a mammalian expression system.
Map data
Sample
  • Virus: Poliovirus 2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE
  • Ligand: water
KeywordsCapsid protein / vaccine / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / receptor-mediated endocytosis of virus by host cell / 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 / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / receptor-mediated endocytosis of virus by host cell / 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 / ribonucleoside triphosphate phosphatase activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
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) / Peptidase C3A/C3B, picornaviral ...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) / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPoliovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsBahar MW / Porta C / Fry EE / Stuart DI
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationRG.IMCB.I8-TSA-083 United States
CitationJournal: Nat Commun / Year: 2025
Title: Recombinant expression systems for production of stabilised virus-like particles as next-generation polio vaccines.
Authors: Lee Sherry / Mohammad W Bahar / Claudine Porta / Helen Fox / Keith Grehan / Veronica Nasta / Helen M E Duyvesteyn / Luigi De Colibus / Johanna Marsian / Inga Murdoch / Daniel Ponndorf / ...Authors: Lee Sherry / Mohammad W Bahar / Claudine Porta / Helen Fox / Keith Grehan / Veronica Nasta / Helen M E Duyvesteyn / Luigi De Colibus / Johanna Marsian / Inga Murdoch / Daniel Ponndorf / Seong-Ryong Kim / Sachin Shah / Sarah Carlyle / Jessica J Swanson / Sue Matthews / Clare Nicol / George P Lomonossoff / Andrew J Macadam / Elizabeth E Fry / David I Stuart / Nicola J Stonehouse / David J Rowlands /
Abstract: Polioviruses have caused crippling disease in humans for centuries, prior to the successful development of vaccines in the mid-1900's, which dramatically reduced disease prevalence. Continued use of ...Polioviruses have caused crippling disease in humans for centuries, prior to the successful development of vaccines in the mid-1900's, which dramatically reduced disease prevalence. Continued use of these vaccines, however, threatens ultimate disease eradication and achievement of a polio-free world. Virus-like particles (VLPs) that lack a viral genome represent a safer potential vaccine, although they require particle stabilization. Using our previously established genetic techniques to stabilize the structural capsid proteins, we demonstrate production of poliovirus VLPs of all three serotypes, from four different recombinant expression systems. We compare the antigenicity, thermostability and immunogenicity of these stabilized VLPs against the current inactivated polio vaccine, demonstrating equivalent or superior immunogenicity in female Wistar rats. Structural analyses of these recombinant VLPs provide a rational understanding of the stabilizing mutations and the role of potential excipients. Collectively, we have established these poliovirus stabilized VLPs as viable next-generation vaccine candidates for the future.
History
DepositionApr 28, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50189.png

Downloads & links

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Map

FileDownload / File: emd_50189.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 506.4 Å		1.06 Å/pix.
x 480 pix.
= 506.4 Å		1.06 Å/pix.
x 480 pix.
= 506.4 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.055 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.643
Minimum - Maximum-1.308588 - 2.5221105
Average (Standard dev.)0.010620236 (±0.14901097)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 506.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50189_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50189_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus 2

EntireName: Poliovirus 2
Components
  • Virus: Poliovirus 2
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: SPHINGOSINE
  • Ligand: water

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Supramolecule #1: Poliovirus 2

SupramoleculeName: Poliovirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Recombinantly expressed virus-like particle of poliovirus type 2 (MEF-1 strain).
NCBI-ID: 12083 / Sci species name: Poliovirus 2 / Sci species strain: MEF-1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.81 MDa
Virus shellShell ID: 1 / Name: Virus shell 1 / Diameter: 310.0 Å / T number (triangulation number): 1

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 2 / Strain: MEF-1
Molecular weightTheoretical: 33.105246 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE TPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSIWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMY I PPGAPIPG ...String:
GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE TPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSIWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMY I PPGAPIPG KWNDYTWQTS SNPSLFYTYG APPARISVPY VGIANAYSHF YDGFAKVPLA GQASTEGDSL YGAASLNDFG SL AVRVVND HNPTKLTSKI RVYMKPKHVR VWCPRPPRAV PYYGPGVDYK DGLAPLPEKG LTTY

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP0

MacromoleculeName: Capsid protein VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 2 / Strain: MEF-1
Molecular weightTheoretical: 37.398816 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYRDSASNA ASKQDFAQDP SKFTEPVKDV LIKTAPTLNS PNIEACGYSD RVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPAVAA CRFYTLDTVT WRKESRGWWW KLPDALKDMG L FGQNMFYH ...String:
MGAQVSSQKV GAHENSNRAY GGSTINYTTI NYYRDSASNA ASKQDFAQDP SKFTEPVKDV LIKTAPTLNS PNIEACGYSD RVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPAVAA CRFYTLDTVT WRKESRGWWW KLPDALKDMG L FGQNMFYH YLGRAGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSTTH MFTKYENANP GEKGGEFKGS FTLDTNATNP AR NFCPVDY LFGSGVLAGN AFVYPHQIIN LRTNNCATLV LPYVNSLSID SMTKHNNWGI AILPLAPLDF ATESSTEIPI TLT IAPMCC EFNGLRNITV PRTQ

UniProtKB: Genome polyprotein

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Macromolecule #3: Capsid protein VP3

MacromoleculeName: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 2 / Strain: MEF-1
Molecular weightTheoretical: 26.457322 KDa
Recombinant expressionOrganism: Mesocricetus auratus (golden hamster)
SequenceString: GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCLSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCLSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRL TINDSFTEGG YISMFYQTRV VVPLSTPRKM DILGFVSACN DFSVRLLRDT THISQEAMPQ

UniProtKB: Genome polyprotein

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Macromolecule #4: SPHINGOSINE

MacromoleculeName: SPHINGOSINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPH
Molecular weightTheoretical: 299.492 Da
Chemical component information

ChemComp-SPH:
SPHINGOSINE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 123 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.62 mg/mL
BufferpH: 7 / Component:
ConcentrationName
1.0 xDPBS
20.0 mMEDTA
/ Details: 1 x DPBS, 20 mM EDTA, pH 7.0
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
Details: The exact grid type was the Ultra-thin carbon support film, 3nm - on lacey carbon. Product code AGS187-4 from Agar Scientific.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV..
DetailsSample purified by sucrose density gradient ultracentrifugation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV / Details: Gatan GIF Quantum energy filter.
DetailsPreliminary grid screening was performed on a Glacios 200 kV microscope.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 1331 / Average exposure time: 10.0 sec. / Average electron dose: 39.08 e/Å2 / Details: Pixel sampling was 1.055 A/pixel.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 47393 / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsEER files were fractionated by 40 fractions.
Particle selectionNumber selected: 18864
Details: Particle picking was performed using the template picker in CryoSPARC.
Startup modelType of model: INSILICO MODEL
In silico model: Five independent 3D models generated in cryoSPARC using ab-initio reconstruction and applying icosahedral symmetry.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Homogeneous reconstruction
Details: Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -67.7 Angstrom squared.
Number images used: 18378
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: ab initio reconstruction
Details: cryoSPARC ab-initio reconstruction uses stochastic gradient descent.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Homogeneous reconstruction
Details: Final angle assignment was achieved by homogeneous refinement procedures in cryoSPARC, which uses branch-and-bound maximum likelihood.
Final 3D classificationNumber classes: 3 / Avg.num./class: 6144 / Software - Name: cryoSPARC (ver. 4.2.1) / Software - details: Heterogeneous reconstruction
Details: Final classification was performed using the heterogeneous reconstruction job in cryoSPARC. 18433 particles used for heterogeneous reconstruction.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1eah


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsInitial model was rigid body fitted using UCSF chimera and Coot. Global minimization and B-factor refinement was performed in real space using phenix_real.space.refine.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9f59:
Poliovirus type 2 (strain MEF-1) stabilised virus-like particle (PV2 SC6b) from a mammalian expression system.

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