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- EMDB-66101: The cryo-electron microscopy complex structure of PCV3 VLPs and a... -

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Basic information

Entry
Database: EMDB / ID: EMD-66101
TitleThe cryo-electron microscopy complex structure of PCV3 VLPs and antibody 2B5
Map data
Sample
  • Complex: PCV3 VLP:2B5 complex
    • Complex: PCV3 cap
      • Protein or peptide: Cap
    • Complex: The Fab of 2B5
      • Protein or peptide: heavy chain of antibody 2B5
      • Protein or peptide: light chain of antibody 2B5
KeywordsPorcine circovirus 3 / Cryo-EM / PCV3 VLP / Immunocomplexes / VIRUS LIKE PARTICLE/IMMUNE SYSTEM / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral capsid assembly / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / DNA binding
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein
Similarity search - Domain/homology
Biological speciesMus (mice) / Porcine circovirus 3
Methodsingle particle reconstruction / cryo EM / Resolution: 1.73 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-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66101.png

Downloads & links

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Map

FileDownload / File: emd_66101.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 640 pix.
= 544. Å		0.85 Å/pix.
x 640 pix.
= 544. Å		0.85 Å/pix.
x 640 pix.
= 544. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.08568758 - 2.0500243
Average (Standard dev.)0.002878668 (±0.034774397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 544.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_66101_additional_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_66101_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66101_half_map_2.map
Projections & Slices
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Sample components

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Entire : PCV3 VLP:2B5 complex

EntireName: PCV3 VLP:2B5 complex
Components
  • Complex: PCV3 VLP:2B5 complex
    • Complex: PCV3 cap
      • Protein or peptide: Cap
    • Complex: The Fab of 2B5
      • Protein or peptide: heavy chain of antibody 2B5
      • Protein or peptide: light chain of antibody 2B5

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Supramolecule #1: PCV3 VLP:2B5 complex

SupramoleculeName: PCV3 VLP:2B5 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus (mice)

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Supramolecule #2: PCV3 cap

SupramoleculeName: PCV3 cap / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: The Fab of 2B5

SupramoleculeName: The Fab of 2B5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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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: 21.000908 KDa
Recombinant expressionOrganism: Baculovirus expression vector pFastBac1-HM
SequenceString:
PTAGTYYTKK YSTMNVISVG TPQDNKPWHA NHFITRLNEW ETAISFEYYK ILKMKVTLSP VISPAQQKKT MFGHTAIDLD GAWTTNTWL QDDPYAESST RKVMTSKKKH SRYFTPKPIL AGTTSAHPGQ SLFFFSRPTP WLNTYDPTVQ WGALLWSIYV P EKTGMTDF YGTKEVWIRY KSVL

UniProtKB: Cap

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Macromolecule #2: heavy chain of antibody 2B5

MacromoleculeName: heavy chain of antibody 2B5 / type: protein_or_peptide / ID: 2
Details: Due to patent protection, we only provide the CDR regions of the antibody that are involved in key interactions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus (mice)
Molecular weightTheoretical: 13.576949 KDa
SequenceString:
QAQLQQPGAE LVRPGASVKL SCKASGYTFS SYWMNWVKQR PEQGLEWIGR IDFYDSENHY NQKFKDKAIL TVDKSSSTAY MQLSSLTSE DSAVYYCAGE SYGNYGRFER WGQGTTLTVS S

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Macromolecule #3: light chain of antibody 2B5

MacromoleculeName: light chain of antibody 2B5 / type: protein_or_peptide / ID: 3
Details: Due to patent protection, we only provide the CDR regions of the antibody that are involved in key interactions.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus (mice)
Molecular weightTheoretical: 11.364478 KDa
SequenceString:
DIVMTQSQKF MSTSVGERVS VTCKASQNVG TNVAWYQQKP GQSPQPLIYS ASYRYSGVPD RFTGSGSGTD FTLTISDVQS EDLAEYFCQ QYNSYPLAFG GGTKL

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.568 µm / Nominal defocus min: 0.3 µm
Experimental equipment
Model: Titan Krios / 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: 1.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 197071
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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