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- EMDB-50835: N-VelcroVax HBcAg in complex with SUMO-gp1 (T=4 VLP) -

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Basic information

Entry
Database: EMDB / ID: EMD-50835
TitleN-VelcroVax HBcAg in complex with SUMO-gp1 (T=4 VLP)
Map dataMap filtered according to local resolution.
Sample
  • Complex: T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO-tagged gp1 from JUNV
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: 3.5 Å
AuthorsFatema K / Snowden JS / Watson A / Sherry L / Ranson NA / Stonehouse NJ / Rowlands DJ
Funding support United Kingdom, 2 items
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, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50835.png

Downloads & links

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Map

FileDownload / File: emd_50835.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap filtered according to local resolution.
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 520 pix.
= 553.8 Å		1.07 Å/pix.
x 520 pix.
= 553.8 Å		1.07 Å/pix.
x 520 pix.
= 553.8 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
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Contour LevelBy AUTHOR: 0.0184
Minimum - Maximum-0.10833122 - 0.20735529
Average (Standard dev.)0.0011874253 (±0.009124514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 553.80005 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50835_msk_1.map
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Mask #2

Fileemd_50835_msk_2.map
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Additional map: Unsharpened map from symmetrised 3D refinement.

Fileemd_50835_additional_1.map
AnnotationUnsharpened map from symmetrised 3D refinement.
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Additional map: Sharpened map (without mask applied) derived from asymmetric...

Fileemd_50835_additional_10.map
AnnotationSharpened map (without mask applied) derived from asymmetric reconstruction of subparticles from a single focussed class, revealing density assigned to complexed SUMO-gp1.
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Additional map: Local resolution values for colouring map by local resolution.

Fileemd_50835_additional_2.map
AnnotationLocal resolution values for colouring map by local resolution.
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Additional map: Sharpened map (with mask applied).

Fileemd_50835_additional_3.map
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Additional map: Sharpened map (without mask applied).

Fileemd_50835_additional_4.map
AnnotationSharpened map (without mask applied).
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Additional map: Half map 1 from asymmetric reconstruction of subparticles...

Fileemd_50835_additional_5.map
AnnotationHalf map 1 from asymmetric reconstruction of subparticles from a single focussed class, revealing density assigned to complexed SUMO-gp1.
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Additional map: Half map 2 from asymmetric reconstruction of subparticles...

Fileemd_50835_additional_6.map
AnnotationHalf map 2 from asymmetric reconstruction of subparticles from a single focussed class, revealing density assigned to complexed SUMO-gp1.
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Additional map: Local resolution-filtered map derived from from asymmetric reconstruction...

Fileemd_50835_additional_7.map
AnnotationLocal resolution-filtered map derived from from asymmetric reconstruction of subparticles from a single focussed class, revealing density assigned to complexed SUMO-gp1.
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AxesZYX

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Additional map: Local resolution values for local resolution-based colouring of...

Fileemd_50835_additional_8.map
AnnotationLocal resolution values for local resolution-based colouring of map derived from asymmetric reconstruction of subparticles from a single focussed class.
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Additional map: Sharpened map (with mask applied) derived from asymmetric...

Fileemd_50835_additional_9.map
AnnotationSharpened map (with mask applied) derived from asymmetric reconstruction of subparticles from a single focussed class, revealing density assigned to complexed SUMO-gp1.
Projections & Slices
AxesZYX

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Half map: Half map 1.

Fileemd_50835_half_map_1.map
AnnotationHalf map 1.
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Half map: Half map 2.

Fileemd_50835_half_map_2.map
AnnotationHalf map 2.
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Sample components

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Entire : T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO...

EntireName: T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO-tagged gp1 from JUNV
Components
  • Complex: T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO-tagged gp1 from JUNV

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Supramolecule #1: T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO...

SupramoleculeName: T=4 virus-like particle of N-VelcroVax HBcAg in complex with SUMO-tagged gp1 from JUNV
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others)

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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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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