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- EMDB-39895: Yeast-expressed polio type 2 stabilized virus-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-39895
TitleYeast-expressed polio type 2 stabilized virus-like particles
Map data
Sample
  • Complex: Poliovirus 2
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
  • Ligand: SPHINGOSINE
KeywordsPoliovirus type 2 / virus-like particles / compact state / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / viral capsid / nucleoside-triphosphate phosphatase ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I 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 / viral capsid / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / host cell cytoplasm / RNA helicase activity / symbiont-mediated suppression of host gene expression / endocytosis involved in viral entry into host cell / 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesPoliovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHong Q / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Vaccines (Basel) / Year: 2024
Title: Vaccine Potency and Structure of Yeast-Produced Polio Type 2 Stabilized Virus-like Particles.
Authors: Qin Hong / Shuxia Wang / Xiaoli Wang / Wenyu Han / Tian Chen / Yan Liu / Fei Cheng / Song Qin / Shengtao Zhao / Qingwei Liu / Yao Cong / Zhong Huang /
Abstract: Poliovirus (PV) is on the brink of eradication due to global vaccination programs utilizing live-attenuated oral and inactivated polio vaccines. Recombinant PV virus-like particles (VLPs) are ...Poliovirus (PV) is on the brink of eradication due to global vaccination programs utilizing live-attenuated oral and inactivated polio vaccines. Recombinant PV virus-like particles (VLPs) are emerging as a safe next-generation vaccine candidate for the impending polio-free era. In this study, we investigate the production, antigenicity, thermostability, immunogenicity, and structures of VLPs derived from PV serotype 2 (PV2) wildtype strain and thermally stabilized mutant (wtVLP and sVLP, respectively). Both PV2 wtVLP and sVLP are efficiently produced in yeast. The PV2 sVLP displays higher levels of D-antigen and significantly enhanced thermostability than the wtVLP. Unlike the wtVLP, the sVLP elicits neutralizing antibodies in mice at levels comparable to those induced by inactivated polio vaccine. The addition of an aluminum hydroxide adjuvant to sVLP results in faster induction and a higher magnitude of neutralizing antibodies. Furthermore, our cryo-EM structural study of both sVLP and wtVLP reveals a native conformation for the sVLP and a non-native expanded conformation for the wtVLP. Our work not only validates the yeast-produced PV2 sVLP as a promising vaccine candidate with high production potential but also sheds light on the structural mechanisms that underpin the assembly and immunogenicity of the PV2 sVLP. These findings may expedite the development of sVLP-based PV vaccines.
History
DepositionApr 26, 2024-
Header (metadata) releaseSep 18, 2024-
Map releaseSep 18, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39895.png

Downloads & links

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Map

FileDownload / File: emd_39895.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 488 pix.
= 533.384 Å		1.09 Å/pix.
x 488 pix.
= 533.384 Å		1.09 Å/pix.
x 488 pix.
= 533.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.047589343 - 0.048275437
Average (Standard dev.)0.000009425523 (±0.0024927824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions488488488
Spacing488488488
CellA=B=C: 533.38403 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_39895_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39895_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_39895_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus 2

EntireName: Poliovirus 2
Components
  • Complex: Poliovirus 2
    • Protein or peptide: VP1
    • Protein or peptide: VP3
    • Protein or peptide: VP2
  • Ligand: SPHINGOSINE

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Supramolecule #1: Poliovirus 2

SupramoleculeName: Poliovirus 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Yeast-expressed polio type 2 stablized virus-like particles
Source (natural)Organism: Poliovirus 2

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 33.073246 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE IPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMF I PPGAPIPG ...String:
GLGDLIEGVV EGVTRNALTP LTPANNLPDT QSSGPAHSKE IPALTAVETG ATNPLVPSDT VQTRHVIQKR TRSESTVESF FARGACVAI IEVDNDAPTK RASKLFSVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT SNYTDANNGH ALNQVYQIMF I PPGAPIPG KWNDYTWQTS SNPSVFYTYG APPARISVPY VGIANAYSHF YDGFAKVPLA GQASTEGDSL YGAASLNDFG SL AVRVVND HNPTKLTSKI RVYMKPKHVR VWCPRPPRAV PYYGPGVDYK DGLAPLPEKG LTTY

UniProtKB: Genome polyprotein

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Macromolecule #2: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 26.49134 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCFSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTADNYQ SPCAIPEFDV TPPIDIPGEV RNMMELAEID TMIPLNLTNQ RKNTMDMYRV ELNDAAHSDT PILCFSLSP ASDPRLAHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA EAPKSRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRL TINDSFTEGG YISMFYQTRV VVPLSTPRKM DILGFVSACN DFSVRLLRDT THISQEAMPQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: picornain 2A
Source (natural)Organism: Poliovirus 2
Molecular weightTheoretical: 29.996779 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: SPNIEACGYS DRVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPDVAA CRFYTLDTVT WRKESRGWWW KLPDALKDM GLFGQNMFYH YLGRAGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSTTH MFTKYENANP GEKGGEFKGS F TLDTNATN ...String:
SPNIEACGYS DRVMQLTLGN STITTQEAAN SVVAYGRWPE YIKDSEANPV DQPTEPDVAA CRFYTLDTVT WRKESRGWWW KLPDALKDM GLFGQNMFYH YLGRAGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSTTH MFTKYENANP GEKGGEFKGS F TLDTNATN PARNFCPVDY LFGSGVLAGN AFVYPHQIIN LRTNNCATLV LPYVNSLSID SMTKHNNWGI AILPLAPLDF AT ESSTEIP ITLTIAPMCC EFNGLRNITV PRTQ

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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Startup model#0 - Type of model: EMDB MAP
#0 - EMDB ID:

3747


#1 - Type of model: EMDB MAP
#1 - EMDB ID:

3747

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Image processing #2

Image processing ID2
Startup model#0 - Type of model: EMDB MAP
#0 - EMDB ID:

3747


#1 - Type of model: EMDB MAP
#1 - EMDB ID:

3747

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9860
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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