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- PDB-9fwe: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus (T=3 VLP) -

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Entry
Database: PDB / ID: 9fwe
TitleN-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus (T=3 VLP)
ComponentsN-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
KeywordsVIRUS LIKE PARTICLE / velcrovax / hepatitis b virus / hepatitis b core antigen / affimer / vaccine / recombinant / vlp / antigen display
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFatema, K. / Snowden, J.S. / Watson, A. / Sherry, L. / Ranson, N.A. / Stonehouse, N.J. / Rowlands, D.J.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust102174/B/13/Z United Kingdom
Wellcome Trust108466/Z/15/Z United Kingdom
CitationJournal: Int J Biol Macromol / Year: 2025
Title: A VLP vaccine platform comprising the core protein of hepatitis B virus with N-terminal antigen capture.
Authors: Kaniz Fatema / Joseph S Snowden / Alexander Watson / Lee Sherry / Neil A Ranson / Nicola J Stonehouse / David J Rowlands /
Abstract: Nanoparticle presentation systems offer the potential to develop new vaccines rapidly in response to emerging diseases, a public health need that has become increasingly evident in the wake of the ...Nanoparticle presentation systems offer the potential to develop new vaccines rapidly in response to emerging diseases, a public health need that has become increasingly evident in the wake of the COVID-19 pandemic. Previously, we reported a nanoparticle scaffold system termed VelcroVax. This was constructed by insertion of a high affinity SUMO binding protein (Affimer), able to recognise a SUMO peptide tag, into the major immunodominant region of VLPs assembled from a tandem (fused dimer) form of hepatitis B virus (HBV) core protein (HBc). Here we describe an alternative form, termed N-VelcroVax, a VLP vaccine platform assembled from a monomeric HBc protein (N-anti-SUMO Affimer HBc 190) with the Affimer inserted at the N-terminus. In contrast to the tandem form of VelcroVax, N-VelcroVax VLPs were expressed well in E. coli. The VLPs effectively bound SUMO-tagged Junín virus glycoprotein, gp1 as assessed by structural and serological analyses. Cryo-EM characterisation of N-VelcroVax complexed with a SUMO-Junín gp1 showed continuous density attributable to the fused Affimer, in addition to evidence of target antigen capture. Collectively, these data suggest that N-VelcroVax has potential as a versatile next generation vaccine scaffold.
History
DepositionJun 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2025Provider: repository / Type: Initial release
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Revision 1.1Mar 5, 2025Group: Data collection / Database references / Category: citation / em_admin / Item: _citation.journal_volume / _em_admin.last_update
Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / Item: _citation.journal_volume / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
B: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
C: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus


Theoretical massNumber of molelcules
Total (without water)102,5163
Polymers102,5163
Non-polymers00
Water00
1
A: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
B: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
C: N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus
x 60


Theoretical massNumber of molelcules
Total (without water)6,150,956180
Polymers6,150,956180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein N-VelcroVax HBcAg with SUMO-Affimer inserted at N-terminus


Mass: 34171.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: T=3 virus-like particle for N-VelcroVax HBcAg / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2900 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 43 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.14_3260: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40254 / Symmetry type: POINT

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