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- EMDB-14370: Ad-DogTag:DogCatcher-RBD -

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Basic information

Entry
Database: EMDB / ID: EMD-14370
TitleAd-DogTag:DogCatcher-RBD
Map dataCryoEM structure of Ad-DogTag:DogCatcher-RBD
Sample
  • Virus: Human adenovirus 5
Biological speciesHuman adenovirus 5
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsDicks MDJ
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mol Ther / Year: 2022
Title: Modular capsid decoration boosts adenovirus vaccine-induced humoral immunity against SARS-CoV-2.
Authors: Matthew D J Dicks / Louisa M Rose / Rebecca A Russell / Lesley A H Bowman / Carl Graham / Jose M Jimenez-Guardeño / Katie J Doores / Michael H Malim / Simon J Draper / Mark Howarth / Sumi Biswas /
Abstract: Adenovirus vector vaccines have been widely and successfully deployed in response to coronavirus disease 2019 (COVID-19). However, despite inducing potent T cell immunity, improvement of vaccine- ...Adenovirus vector vaccines have been widely and successfully deployed in response to coronavirus disease 2019 (COVID-19). However, despite inducing potent T cell immunity, improvement of vaccine-specific antibody responses upon homologous boosting is modest compared with other technologies. Here, we describe a system enabling modular decoration of adenovirus capsid surfaces with antigens and demonstrate potent induction of humoral immunity against these displayed antigens. Ligand attachment via a covalent bond was achieved using a protein superglue, DogTag/DogCatcher (similar to SpyTag/SpyCatcher), in a rapid and spontaneous reaction requiring only co-incubation of ligand and vector components. DogTag was inserted into surface-exposed loops in the adenovirus hexon protein to allow attachment of DogCatcher-fused ligands on virus particles. Efficient coverage of the capsid surface was achieved using various ligands, with vector infectivity retained in each case. Capsid decoration shielded particles from vector neutralizing antibodies. In prime-boost regimens, adenovirus vectors decorated with the receptor-binding domain of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike induced >10-fold higher SARS-CoV-2 neutralization titers compared with an undecorated vector encoding spike. Importantly, decorated vectors achieved equivalent or superior T cell immunogenicity against encoded antigens compared with undecorated vectors. We propose capsid decoration using protein superglues as a novel strategy to improve efficacy and boostability of adenovirus-based vaccines and therapeutics.
History
DepositionFeb 17, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14370.png

Downloads & links

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Map

FileDownload / File: emd_14370.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM structure of Ad-DogTag:DogCatcher-RBD
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.19 Å/pix.
x 288 pix.
= 1494.72 Å		5.19 Å/pix.
x 288 pix.
= 1494.72 Å		5.19 Å/pix.
x 288 pix.
= 1494.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-3.888648 - 4.4579563
Average (Standard dev.)-0.021553824 (±0.56286556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 1494.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human adenovirus 5

EntireName: Human adenovirus 5
Components
  • Virus: Human adenovirus 5

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Supramolecule #1: Human adenovirus 5

SupramoleculeName: Human adenovirus 5 / type: virus / ID: 1 / Parent: 0
Details: Human adenovirus 5 particle displaying the receptor binding domain (RBD) of SARS CoV-2 spike on the surface of the adenovirus capsid. Adenovirus component produced in HEK293 cells, RBD ...Details: Human adenovirus 5 particle displaying the receptor binding domain (RBD) of SARS CoV-2 spike on the surface of the adenovirus capsid. Adenovirus component produced in HEK293 cells, RBD component produced in CHO-S cells. Components conjugated in vitro using DogTag/DogCatcher protein superglue.
NCBI-ID: 28285 / Sci species name: Human adenovirus 5 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 10.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28307
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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