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- PDB-9wmr: Cryo-EM structure of PCV3 VLPs -

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Basic information

Entry
Database: PDB / ID: 9wmr
TitleCryo-EM structure of PCV3 VLPs
ComponentsCap
KeywordsVIRUS LIKE PARTICLE / Porcine circovirus 3 / Cryo-EM / PCV3 VLP
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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 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: Su, J. / Tong, X. / Jiang, Y. / Li, Y. / Yan, H. / Liu, Y. / Wang, Y. / Su, X. / Sun, Z. / Wang, M. / Xia, N. / Bostina, M. / Li, S. / Pang, W. / Zheng, Q. / Tian, K.
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: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cap


Theoretical massNumber of molelcules
Total (without water)25,1461
Polymers25,1461
Non-polymers00
Water00
1


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

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Components

#1: Protein Cap


Mass: 25145.807 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
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

ComponentName: Porcine circovirus 3 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Porcine circovirus 3
Source (recombinant)Organism: Baculovirus expression vector pFastBac1-HM
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 9.6
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: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3872 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39064 / Symmetry type: POINT

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