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- EMDB-65817: Yeast-expressed polio type 1 expanded virus-like particles -

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Basic information

Entry
Database: EMDB / ID: EMD-65817
TitleYeast-expressed polio type 1 expanded virus-like particles
Map data
Sample
  • Complex: Poliovirus 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3
KeywordsPoliovirus type 1 / virus-like particles / expanded state / VIRAL PROTEIN / 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 / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...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 / 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 / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / 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 / 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
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 / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / 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 speciesHomo sapiens (human) / Poliovirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsHong Q / Cong Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: NPJ Vaccines / Year: 2026
Title: Structural insight into the assembly and D antigenicity of polio type 1 stabilized virus-like particles.
Authors: Qin Hong / Tian Chen / Wenyu Han / Shuxia Wang / Chaoyang Lian / Yujie Zhang / Lizhu Ruan / Tingfeng Wang / Cheng Lin / Congcong Song / Qingwei Liu / Xiaoli Wang / Yao Cong / Zhong Huang /
Abstract: The inherent instability of poliovirus capsids presents a formidable challenge for developing next-generation vaccines suitable for a post-eradication world. Here, we address this by engineering a ...The inherent instability of poliovirus capsids presents a formidable challenge for developing next-generation vaccines suitable for a post-eradication world. Here, we address this by engineering a thermally stabilized virus-like particle (sVLP) derived from the poliovirus serotype 1 (PV1) Mahoney-SC7 mutant and elucidating its atomic-level structure. Produced at remarkably high yields in Pichia pastoris yeast, our engineered sVLP maintains a native, D-antigenic conformation and elicits a potent neutralizing antibody response in mice, in sharp contrast to unstable wild-type VLP (wtVLP) which adopts an expanded, non-immunogenic form. Our 2.43 Å resolution cryo-EM structure reveals precisely how seven stabilizing mutations cooperatively enhance inter-protomer contacts and rigidify surface loops to lock the particle in its immunogenic state. We further define a critical D-antigenic epitope by determining the 2.60 Å structure of the sVLP in complex with a novel D-antigen-specific, neutralizing monoclonal antibody, 3G10, elucidating the structural mechanisms of D-antigen recognition and virus neutralization by 3G10. These findings provide a definitive structural blueprint for engineering stable, immunogenic vaccines for PVs and other enteroviruses and also deliver a vital reagent for ensuring vaccine quality control.
History
DepositionAug 12, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65817.png

Downloads & links

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Map

FileDownload / File: emd_65817.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.093 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0271
Minimum - Maximum-0.030166006 - 1.2309377
Average (Standard dev.)0.0037067274 (±0.041903034)
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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Half map: #1

Fileemd_65817_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_65817_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Poliovirus 1

EntireName: Poliovirus 1
Components
  • Complex: Poliovirus 1
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Capsid protein VP2
    • Protein or peptide: Capsid protein VP3

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Supramolecule #1: Poliovirus 1

SupramoleculeName: Poliovirus 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Yeast-expressed polio type 1 expanded virus-like particles
Source (natural)Organism: Homo sapiens (human)

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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 1
Molecular weightTheoretical: 33.478578 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNSASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE ...String:
GLGQMLESMI DNTVRETVGA ATSRDALPNT EASGPTHSKE IPALTAVETG ATNPLVPSDT VQTRHVVQHR SRSESSIESF FARGACVTI MTVDNSASTT NKDKLFAVWK ITYKDTVQLR RKLEFFTYSR FDMELTFVVT ANFTETNNGH ALNQVYQIMY V PPGAPVPE KWDDYTWQTS SNPSIFYTYG TAPARISVPY VGISNAYSHF YDGFSKVPLK DQSAALGDSL YGAASLNDFG IL AVRVVND HNPTKVTSKI RVYLKPKHIR VWCPRPPRAV AYYGPGVDYK DGTLTPLSTK DLTTY

UniProtKB: Genome polyprotein

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Macromolecule #2: Capsid protein VP2

MacromoleculeName: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Poliovirus 1
Molecular weightTheoretical: 30.075783 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT ...String:
SPNIEACGYS DRVLQLTLGN STITTQEAAN SVVAYGRWPE YLRDSEANPV DQPTEPDVAA CRFYTLDTVS WTKESRGWWW KLPDALRDM GLFGQNMYYH YLGRSGYTVH VQCNASKFHQ GALGVFAVPE MCLAGDSNTT TMHTSYQNAN PGEKGGTFTG T FTPDNNQT SPARRFCPVD YLLGNGTLLG NAFVFPHQII NLRTNNCATL VLPYVNSLSI DSMVKHNNWG IAILPLAPLN FA SESSPEI PITLTIAPMC 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: Poliovirus 1
Molecular weightTheoretical: 26.547482 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV ...String:
GLPVMNTPGS NQYLTADNFQ SPCALPEFDV TPPIDIPGEV KNMMELAEID TMIPFDLSAT KKNTMEMYRV RLSDKPHTDD PILCLSLSP ASDPRLSHTM LGEILNYYTH WAGSLKFTFL FCGSMMATGK LLVSYAPPGA DPPKKRKEAM LGTHVIWDIG L QSSCTMVV PWISNTTYRQ TIDDSFTEGG YISVFYQTRI VVPLSTPREM DILGFVSACN DFSVRLLRDT THIEQKALAQ

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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TECNAI F30
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: Tecnai F30 / Image courtesy: FEI Company

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Image processing

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

60095

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 211442
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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