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- EMDB-81988: Yeast-expressed polio type 3 stabilized virus-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-81988
TitleYeast-expressed polio type 3 stabilized virus-like particles
Map datadeepEMhancer-processed map
Sample
  • Virus: Poliovirus 3
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3
KeywordsPoliovirus type 3 / virus-like particles / stabilized state / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / viral capsid / host cell cytoplasm / symbiont-mediated suppression of host gene expression / virion attachment to host cell / structural molecule activity
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
Biological speciesPoliovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsHong Q / Cong Y
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32130056 China
National Natural Science Foundation of China (NSFC)32570924 China
CitationJournal: Antiviral Res / Year: 2026
Title: High-yield production of immunogenic PV3 virus-like particle in yeast.
Authors: Tian Chen / Qin Hong / Wenyu Han / Shuxia Wang / Cheng Lin / Jiaqi Yao / Chaoyang Lian / Qingwei Liu / Xiaoli Wang / Yanqiu Zhou / Yao Cong / Zhong Huang /
Abstract: The identification of thermally stabilized mutants of all three poliovirus serotypes (PV1, PV2, and PV3) has enabled the development of virus-like particle (VLP)-based next-generation poliovirus ...The identification of thermally stabilized mutants of all three poliovirus serotypes (PV1, PV2, and PV3) has enabled the development of virus-like particle (VLP)-based next-generation poliovirus vaccines. PV3 stabilized mutant-derived VLPs (sVLPs) have been produced in several recombinant systems through co-expression of mutant P1 polyprotein with native or uncleavable viral protease 3CD, and have shown immunogenicity in animal models. However, their yields remain suboptimal, likely because of intrinsic 3CD toxicity and/or inefficient 3CD-mediated cleavage of P1 into capsid subunits VP0, VP3, and VP1, creating a bottleneck for cost-effective product development. In this study, we designed a protease-independent expression strategy based on simultaneous co-expression of VP0, VP3, and VP1 capsid subunit (VP0/VP3/VP1) and compared it with the conventional P1/3CD co-expression approach for production of PV3 sVLP and wildtype VLP (wtVLP) in Pichia pastoris. For each VLP type, the VP0/VP3/VP1 strategy in general enhances target protein expression and D-antigen formation compared with P1/3CD co-expression. The PV3 sVLP produced by the VP0/VP3/VP1 strategy possesses higher levels of D-antigen and significantly enhanced thermostability than the corresponding wtVLP. Moreover, structural and immunological analyses reveal that PV3 sVLP, but not wtVLP, adopts a native conformation and potently elicits neutralizing antibodies in a mouse model. These findings not only confirm yeast-produced PV3 sVLP as a promising vaccine candidate, but also establish a high-yield and scalable expression strategy amenable to further development and industrial-level production of sVLP-based next-generation polio vaccines.
History
DepositionJul 8, 2026-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_81988.png

Downloads & links

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Map

FileDownload / File: emd_81988.map.gz / Format: CCP4 / Size: 443.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationdeepEMhancer-processed map
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

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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: 0.162
Minimum - Maximum-0.002409425 - 1.705773
Average (Standard dev.)0.005689674 (±0.05484476)
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: Density map from 3D refinement

Fileemd_81988_additional_1.map
AnnotationDensity map from 3D refinement
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_81988_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_81988_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus 3

EntireName: Poliovirus 3
Components
  • Virus: Poliovirus 3
    • Protein or peptide: VP1
    • Protein or peptide: VP2
    • Protein or peptide: VP3

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Supramolecule #1: Poliovirus 3

SupramoleculeName: Poliovirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12086 / Sci species name: Poliovirus 3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 33.562785 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW ...String:
GIEDLITEVA QGALTLSLPK QQDSLPDTKA SGPAHSKEVP ALTAVETGAT NPLVPSDTVQ TRHVIQRRSR SESTIESFFA RGACVAIIE VDNEEPTTRA QKLFAMWRIT YKDTVQLRRK LEFFTYSRFD MELTFVVTAN FTNTNNGHAL NQVYQIMYIP P GAPTPKSW DDYTWQTSSN PSIFYTYGAA PARISVPYVG LANAYSHFYD GFAKVPLKTD ANDQIGDSLY SAMTVDDFGV LA IRVVNDH NPTKVTSKVR IYMKPKHVRV WCPRPPRAVP YYGPGVDYKD NLNPLSEKGL TTY

UniProtKB: Genome polyprotein

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Macromolecule #2: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 30.188982 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: SPNVEACGYS DRVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ F NRDTAVTS ...String:
SPNVEACGYS DRVLQLTIGN STITTQEAAN SVVAYGRWPE FIRDDEANPV DQPTEPDVAT CRFYTLDTVM WGKESKGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAIPE YCLAGDSDKQ RYTSYANANP GEKGGKFYSQ F NRDTAVTS PKREFCPVDY LLGCGVLLGN AFVYPHQIIN LRTNNSATIV LPYVNAMAID SMVKHNNWGI AILPLSPLDF AQ ESSVEIP ITVTIAPMCS EFNGLRNVTA PKFQ

UniProtKB: Genome polyprotein

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 3
Molecular weightTheoretical: 26.3151 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV ...String:
GLPVLNTPGS NQYLTSDNYQ SPCAIPEFDV TPPIDIPGEV KNMMELAEID TMIPLNLENT KRNTMDMYRV TLSDSADLSQ PILCFSLSP ASDPRLSHTM LGEVLNYYTH WAGSLKFTFL FCGSMMATGK ILVAYAPPGA QPPTSRKEAM LGTHVIWDLG L QSSCTMVV PWISNVTYRQ TTQDSFTEGG YISMFYQTRI VVPLSTPKSM SMLGFVSACN DFSVRLLRDT THISQSALPQ

UniProtKB: Genome polyprotein

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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

MicroscopeTFS TALOS
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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

3747

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 50980
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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