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- EMDB-66102: Cryo-EM structure of PCV3 VLPs -

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Basic information

Entry
Database: EMDB / ID: EMD-66102
TitleCryo-EM structure of PCV3 VLPs
Map data
Sample
  • Virus: Porcine circovirus 3
    • Protein or peptide: Cap
KeywordsPorcine circovirus 3 / Cryo-EM / PCV3 VLP / VIRUS LIKE PARTICLE
Biological speciesPorcine circovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsSu J / Jiang Y / Li S / Zheng Q
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis and immunogenic efficacy of porcine circovirus type 3 virus-like particle.
Authors: Jinfu Su / Xiaodan Tong / Yanan Jiang / Yu Li / He Yan / Yan Liu / Yanwei Wang / Xiaorui Su / Zhe Sun / Mengyue Wang / Ningshao Xia / Mihnea Bostina / Shaowei Li / Wenqiang Pang / Qingbing ...Authors: Jinfu Su / Xiaodan Tong / Yanan Jiang / Yu Li / He Yan / Yan Liu / Yanwei Wang / Xiaorui Su / Zhe Sun / Mengyue Wang / Ningshao Xia / Mihnea Bostina / Shaowei Li / Wenqiang Pang / Qingbing Zheng / Kegong Tian /
Abstract: Porcine circovirus type 3 (PCV3) is an emerging swine pathogen associated with reproductive failure and systemic inflammation, but vaccines for related PCV2 provide limited cross-protection. Here, we ...Porcine circovirus type 3 (PCV3) is an emerging swine pathogen associated with reproductive failure and systemic inflammation, but vaccines for related PCV2 provide limited cross-protection. Here, we determine high-resolution cryo-EM structures of PCV3 capsid protein assembled into virus-like particles (VLPs) and of PCV3 VLPs bound to the PCV3-specific antibody 2B5. The structures reveal differences from PCV2 in surface loops and define a conserved 2B5 epitope mainly involving the BC, EF and HI loops, providing a structural basis for PCV3-specific recognition. PCV3 VLPs induce sustained antibody responses in mice and pigs. In a pig challenge model, VLP immunization prevents viremia and viral replication in lungs and lymph nodes, as measured by quantitative PCR and in situ hybridization, with protection maintained for at least five months after boosting. These findings support PCV3 VLPs as a vaccine candidate against PCV3 infection.
History
DepositionSep 3, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66102.png

Downloads & links

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Map

FileDownload / File: emd_66102.map.gz / Format: CCP4 / Size: 103 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 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.0257192 - 1.7211378
Average (Standard dev.)0.011116627 (±0.1174568)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66102_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_66102_half_map_2.map
Projections & Slices
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Sample components

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Entire : Porcine circovirus 3

EntireName: Porcine circovirus 3
Components
  • Virus: Porcine circovirus 3
    • Protein or peptide: Cap

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Supramolecule #1: Porcine circovirus 3

SupramoleculeName: Porcine circovirus 3 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1868221 / Sci species name: Porcine circovirus 3 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Cap

MacromoleculeName: Cap / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porcine circovirus 3
Molecular weightTheoretical: 25.145807 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString: MVYRRRRRSS TGTTYGSTRR RRYARRRLFI RRPTAGTYYT KKYSTMNVIS VGTPQDNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ KKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR ...String:
MVYRRRRRSS TGTTYGSTRR RRYARRRLFI RRPTAGTYYT KKYSTMNVIS VGTPQDNKPW HANHFITRLN EWETAISFEY YKILKMKVT LSPVISPAQQ KKTMFGHTAI DLDGAWTTNT WLQDDPYAES STRKVMTSKK KHSRYFTPKP ILAGTTSAHP G QSLFFFSR PTPWLNTYDP TVQWGALLWS IYVPEKTGMT DFYGTKEVWI RYKSVL

UniProtKB: Cap

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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: 9.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.872 µm / Nominal defocus min: 0.3 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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 39064
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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