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- EMDB-50176: Poliovirus type 1 (strain Mahoney) stabilised virus-like particle... -

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Basic information

Entry
Database: EMDB / ID: EMD-50176
TitlePoliovirus type 1 (strain Mahoney) stabilised virus-like particle (PV1 SC6b) in complex with GPP3 and GSH.
Map data
Sample
  • Virus: Human poliovirus 1 Mahoney
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE
  • Ligand: GLUTATHIONE
KeywordsCapsid protein / virus-like particle / inhibitor / complex / vaccine / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont-mediated suppression of host translation initiation / 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 / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid ...symbiont-mediated suppression of host translation initiation / 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 / picornain 2A / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / endocytosis involved in viral entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / 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
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 speciesHuman poliovirus 1 Mahoney
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsBahar MW / Nasta V / Sherry L / Stonehouse NJ / Rowlands DJ / 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 25, 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_50176.png

Downloads & links

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Map

FileDownload / File: emd_50176.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å		1.08 Å/pix.
x 448 pix.
= 483.84 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.7
Minimum - Maximum-4.2676344 - 7.1320834
Average (Standard dev.)0.031745695 (±0.4177376)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 483.84003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_50176_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_50176_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human poliovirus 1 Mahoney

EntireName: Human poliovirus 1 Mahoney
Components
  • Virus: Human poliovirus 1 Mahoney
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP0
    • Protein or peptide: Capsid protein VP3
  • Ligand: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE
  • Ligand: GLUTATHIONE

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Supramolecule #1: Human poliovirus 1 Mahoney

SupramoleculeName: Human poliovirus 1 Mahoney / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Recombinantly expressed virus-like particle of poliovirus type 1 (Mahoney strain).
NCBI-ID: 12081 / Sci species name: Human poliovirus 1 Mahoney / Sci species strain: Mahoney / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 5.84 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: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 33.447586 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE ...String:
GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNPASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE KWDDYTWQTS SNPSIFYTYG TAPARISVPY VGISNAYSHF YDGFSKVPLK DQSAALGDSL YGAASLNDFG IL AVRVVND PNPTKVTSKI RVYLKPKHIR VWCPRPPRAV AYYGPGVDYK DGTLTPLSTK DLTTY

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: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 37.465812 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MGAQVSSQKV GAHENSNGAY GGSTINYTTI NYYRDSASNA ASKQDFSQDP SKFTEPIKDV LIKTAPMLNS PNIEACGYSD RVLQLTLGN STITAQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPEVAA CRFYTLDTVS WTKESRGWWW KLPDALRDMG L FGQNMYYH ...String:
MGAQVSSQKV GAHENSNGAY GGSTINYTTI NYYRDSASNA ASKQDFSQDP SKFTEPIKDV LIKTAPMLNS PNIEACGYSD RVLQLTLGN STITAQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPEVAA CRFYTLDTVS WTKESRGWWW KLPDALRDMG L FGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG TFTPDNNQTS PA RRFCPVD YLLGNGTLLG NAFVFPHQII NLRTNNCATL VLPYVNSLSI DSMVKHNNWG IAILPLAPLN FASESSPEIP ITL TIAPMC CEFNGLRNIT LPRLQ

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: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 26.550549 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFM FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFM FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRL TIDDSFTEGG YISVFYQTRI VVPLSTPREM DILGFVSACN DFSVRLLRDT THIEQKALAQ

UniProtKB: Genome polyprotein

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Macromolecule #4: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-P...

MacromoleculeName: 1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE
type: ligand / ID: 4 / Number of copies: 1 / Formula: YM2
Molecular weightTheoretical: 410.509 Da
Chemical component information

ChemComp-YM2:
1-[(3S)-5-[4-[(E)-ETHOXYIMINOMETHYL]PHENOXY]-3-METHYL-PENTYL]-3-PYRIDIN-4-YL-IMIDAZOLIDIN-2-ONE

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Macromolecule #5: GLUTATHIONE

MacromoleculeName: GLUTATHIONE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GSH
Molecular weightTheoretical: 307.323 Da
Chemical component information

ChemComp-GSH:
GLUTATHIONE

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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

Concentration0.1 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 / 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 used was Ultra-thin carbon support film, 3nm - on lacey carbon (product AGS187-4, Agar Scientific).
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3-4 ul of sample blotted for 3.5 seconds with -15 blot force on FEI Vitrobot mark IV..
DetailsSample purified by sucrose density gradient ultracentrifugation. Concentrated sample mixed with GPP3 and GSH (10mM final) to form complex.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsCalibrated pixel size was 1.08 A/pix.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 4467 / Average exposure time: 0.77 sec. / Average electron dose: 35.49 e/Å2
Details: Pixel sampling was 1.08 A/pixel. Images collected in linear mode on Falcon 3.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 129629 / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 75000
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

Particle selectionNumber selected: 159830
Details: Particle picking performed in cryoSPARC using the blob picker.
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: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Icosahedral symmetry applied to final reconstruction. Final maps were post-processed with an inverse B-factor of -146.7 Angstrom squared.
Number images used: 23721
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.2.1)
Details: cryoSPARC ab-initio reconstruction uses stochastic gradient descent.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Details: Final angle assignment was achieved by homogeneous refinement procedures in cryoSPARC, which uses branch-and-bound maximum likelihood.
Final 3D classificationNumber classes: 5 / Avg.num./class: 4752 / Software - Name: cryoSPARC (ver. 4.2.1) / Details: 23763 particles used for ab-initio reconstruction.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1hxs


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: UCSF Chimera (ver. 1.16)
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-9f3q:
Poliovirus type 1 (strain Mahoney) stabilised virus-like particle (PV1 SC6b) in complex with GPP3 and GSH.

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