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- EMDB-66101: Unknown entry -

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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
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: 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, 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_66101.png

Downloads & links

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Map

FileReleased
Voxel sizeX=Y=Z: 0.85 Å
Density
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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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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