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- EMDB-14868: VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR (T=3* VLP) -

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Basic information

Entry
Database: EMDB / ID: EMD-14868
TitleVelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR (T=3* VLP)
Map dataDensity map filtered by local resolution.
Sample
  • Complex: T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
    • Protein or peptide: VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
KeywordsVelcroVax / Hepatitis B virus / Hepatitis B core antigen / Affimer / Vaccine / Recombinant / VLP / Antigen display / VIRUS LIKE PARTICLE
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKingston NJ / Grehan K / Snowden JS / Alzahrani J / Ranson NA / Rowlands DJ / Stonehouse NJ
Funding support United Kingdom, United States, 4 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/P022626/1 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI 169457-0 United States
Wellcome Trust204825/Z/16/Z United Kingdom
Wellcome Trust102174/B/13/Z United Kingdom
CitationJournal: mSphere / Year: 2023
Title: VelcroVax: a "Bolt-On" Vaccine Platform for Glycoprotein Display.
Authors: Natalie J Kingston / Keith Grehan / Joseph S Snowden / Mark Hassall / Jehad Alzahrani / Guido C Paesen / Lee Sherry / Connor Hayward / Amy Roe / Sam Stephen / Darren Tomlinson / Antra ...Authors: Natalie J Kingston / Keith Grehan / Joseph S Snowden / Mark Hassall / Jehad Alzahrani / Guido C Paesen / Lee Sherry / Connor Hayward / Amy Roe / Sam Stephen / Darren Tomlinson / Antra Zeltina / Katie J Doores / Neil A Ranson / Martin Stacey / Mark Page / Nicola J Rose / Thomas A Bowden / David J Rowlands / Nicola J Stonehouse /
Abstract: Having varied approaches to the design and manufacture of vaccines is critical in being able to respond to worldwide needs and newly emerging pathogens. Virus-like particles (VLPs) form the basis of ...Having varied approaches to the design and manufacture of vaccines is critical in being able to respond to worldwide needs and newly emerging pathogens. Virus-like particles (VLPs) form the basis of two of the most successful licensed vaccines (against hepatitis B virus [HBV] and human papillomavirus). They are produced by recombinant expression of viral structural proteins, which assemble into immunogenic nanoparticles. VLPs can be modified to present unrelated antigens, and here we describe a universal "bolt-on" platform (termed VelcroVax) where the capturing VLP and the target antigen are produced separately. We utilize a modified HBV core (HBcAg) VLP with surface expression of a high-affinity binding sequence (Affimer) directed against a SUMO tag and use this to capture SUMO-tagged gp1 glycoprotein from the arenavirus Junín virus (JUNV). Using this model system, we have solved the first high-resolution structures of VelcroVax VLPs and shown that the VelcroVax-JUNV gp1 complex induces superior humoral immune responses compared to the noncomplexed viral protein. We propose that this system could be modified to present a range of antigens and therefore form the foundation of future rapid-response vaccination strategies. The hepatitis B core protein (HBc) forms noninfectious virus-like particles, which can be modified to present a capturing molecule, allowing suitably tagged antigens to be bound on their surface. This system can be adapted and provides the foundation for a universal "bolt-on" vaccine platform (termed VelcroVax) that can be easily and rapidly modified to generate nanoparticle vaccine candidates.
History
DepositionApr 29, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateAug 9, 2023-
Current statusAug 9, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14868.png

Downloads & links

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Map

FileDownload / File: emd_14868.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity map filtered by local resolution.
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 460 pix.
= 489.9 Å		1.07 Å/pix.
x 460 pix.
= 489.9 Å		1.07 Å/pix.
x 460 pix.
= 489.9 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0926607 - 0.20234554
Average (Standard dev.)0.00085723447 (±0.0099067455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 489.90002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14868_msk_1.map
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Additional map: Sharpened map with mask applied to exclude solvent.

Fileemd_14868_additional_1.map
AnnotationSharpened map with mask applied to exclude solvent.
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Additional map: Unsharpened map derived from 3D refinement.

Fileemd_14868_additional_2.map
AnnotationUnsharpened map derived from 3D refinement.
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Additional map: Sharpened map.

Fileemd_14868_additional_3.map
AnnotationSharpened map.
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Half map: Half map 1.

Fileemd_14868_half_map_1.map
AnnotationHalf map 1.
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Half map: Half map 2.

Fileemd_14868_half_map_2.map
AnnotationHalf map 2.
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Sample components

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Entire : T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Aff...

EntireName: T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
Components
  • Complex: T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
    • Protein or peptide: VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR

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Supramolecule #1: T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Aff...

SupramoleculeName: T=3* virus-like particle for VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR

MacromoleculeName: VelcroVax tandem HBcAg with SUMO-Affimer inserted at MIR
type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 52.79277 KDa
Recombinant expressionOrganism: Komagataella phaffii (fungus)
SequenceString: MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEGSM ASAATGVRA VPGNENSLEI EELARFAVDE HNKKENALLE FVRVVKAKEQ IIIHENDADT MYYLTLEAKD GGKKKLYEAK V WVKGIMDG ...String:
MDIDPYKEFG ATVELLSFLP SDFFPSVRDL LDTASALYRE ALESPEHCSP HHTALRQAIL CWGELMTLAT WVGNNLEGSM ASAATGVRA VPGNENSLEI EELARFAVDE HNKKENALLE FVRVVKAKEQ IIIHENDADT MYYLTLEAKD GGKKKLYEAK V WVKGIMDG LNKYNFKELQ EFKPVGDAGG RDPASRDLVV NYVNTNMGLK IRQLLWFHIS CLTFGRETVL EYLVSFGVWI RT PPAYRPP NAPILSTLPE TTVVGGSSGG SGGSGGSGGS GGSGGSTMDI DPYKEFGATV ELLSFLPSDF FPSVRDLLDT ASA LYREAL ESPEHCSPHH TALRQAILCW GELMTLATWV GNNLEFAGAS DPASRDLVVN YVNTNMGLKI RQLLWFHISC LTFG RETVL EYLVSFGVWI RTPPAYRPPN APILSTLPET TVVRRRDRGR SPRRRTPSPR RRRSQSPRRR RSQSRESQC

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 60.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 51376
FSC plot (resolution estimation)

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