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- PDB-9wmq: The cryo-electron microscopy complex structure of PCV3 VLPs and a... -

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Basic information

Entry
Database: PDB / ID: 9wmq
TitleThe cryo-electron microscopy complex structure of PCV3 VLPs and antibody 2B5
Components
  • Cap
  • heavy chain of antibody 2B5
  • light chain of antibody 2B5
KeywordsVIRUS LIKE PARTICLE/IMMUNE SYSTEM / Porcine circovirus 3 / Cryo-EM / PCV3 VLP / Immunocomplexes / 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 speciesPorcine circovirus 3
Mus (mice)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.73 Å
AuthorsSu, J. / Jiang, Y. / Li, S. / Zheng, Q.
Funding support1items
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, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2026Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.1Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Cap
H: heavy chain of antibody 2B5
L: light chain of antibody 2B5


Theoretical massNumber of molelcules
Total (without water)45,9423
Polymers45,9423
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cap


Mass: 21000.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 3 / Gene: ORF2 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: A0A6B9EZK0
#2: Antibody heavy chain of antibody 2B5


Mass: 13576.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Due to patent protection, we only provide the CDR regions of the antibody that are involved in key interactions.
Source: (natural) Mus (mice)
#3: Antibody light chain of antibody 2B5


Mass: 11364.478 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: Due to patent protection, we only provide the CDR regions of the antibody that are involved in key interactions.
Source: (natural) Mus (mice)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1PCV3 VLP:2B5 complexCOMPLEXall0MULTIPLE SOURCES
2PCV3 capCOMPLEX#11RECOMBINANT
3The Fab of 2B5COMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus (mice)10088
31Porcine circovirus 31868221
41Mus (mice)10088
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1568 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 1.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197071 / Symmetry type: POINT

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