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- EMDB-55303: Adenovirus dodecahedron -

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Basic information

Entry
Database: EMDB / ID: EMD-55303
TitleAdenovirus dodecahedron
Map dataChimpSELS Addomer map
Sample
  • Complex: Adenovirus dodecahedron
    • Protein or peptide: Penton protein
  • Ligand: POTASSIUM ION
Keywordsadenovirus / virus like particle / vaccine / dodecahedron
Function / homologyAdenovirus penton base protein / Adenovirus penton base protein / T=25 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity / Penton protein
Function and homology information
Biological speciesChimpanzee adenovirus Y25
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKabasakal BV / Buzas D / Bufton J / Berger-Schaffitzel C / Berger I
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Wellcome Trust210701/Z/18/Z; 106115/Z/14/Z; 202904/Z/16/Z; 206181/Z/17/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000484/1 United Kingdom
Engineering and Physical Sciences Research CouncilEP/R013764/1 United Kingdom
CitationJournal: ACS Synth Biol / Year: 2026
Title: Engineering the ADDomer Nanoparticle Vaccine Scaffold for Improved Assembly and Enhanced Stability.
Authors: Georgia Balchin / Burak V Kabasakal / Alessandro Strofaldi / Sophie Hall / Charlotte Fletcher / Dora Buzas / Joshua C Bufton / Sathish K N Yadav / Dakang Shen / Frederic Garzoni / H Adrian ...Authors: Georgia Balchin / Burak V Kabasakal / Alessandro Strofaldi / Sophie Hall / Charlotte Fletcher / Dora Buzas / Joshua C Bufton / Sathish K N Yadav / Dakang Shen / Frederic Garzoni / H Adrian Bunzel / Jennifer J McManus / Christiane Schaffitzel / Imre Berger /
Abstract: Virus-like particles (VLPs) are promising platforms for next-generation vaccines due to their ability to present antigens in highly ordered, repetitive geometries emulating pathogen-associated ...Virus-like particles (VLPs) are promising platforms for next-generation vaccines due to their ability to present antigens in highly ordered, repetitive geometries emulating pathogen-associated patterns to elicit potent immune responses. The ADDomer is a synthetic dodecahedral VLP scaffold derived from the penton base protein (PBP) of human adenovirus serotype 3 (Ad3). PBP tolerates insertion of multiple antigenic epitopes in flexible surface-exposed loops, and spontaneously self-assembles into ADDomer nanoparticles, but faces limitations including incomplete assembly and susceptibility to preexisting antihuman adenovirus immunity. Here, we report two complementary engineering strategies to enhance ADDomer robustness. First, we developed a Chimpanzee adenovirus Y25-based ADDomer (CHIMPSELS) to circumvent preexisting antihuman adenovirus immunity, and introduced a point mutation to restore a motif critical for dodecahedron integrity. Second, we introduced targeted intersubunit disulfide bonds to reinforce particle assembly. High-resolution electron cryo-microscopy confirmed the formation of intact dodecahedral particles, revealing that disulfide bonds stabilize distinct conformations of the PBP N-termini. Differential scanning fluorimetry and dynamic light scattering demonstrated thermal stability and elevated aggregation onset temperatures in the disulfide-stabilized ADDomers, providing a scalable assay for screening ADDomer-based VLP constructs for vaccine development. Incorporation of validated immunogenic epitopes, including a SARS-CoV-2 receptor-binding motif segment and the Chikungunya E2EP3 peptide, demonstrated structural integrity and epitope display by the modified scaffolds. Our results establish a versatile, thermostable VLP platform with reduced susceptibility to preexisting immunity, improved particle integrity, and capacity for modular epitope presentation. This work advances the ADDomer toward practical applications in vaccine development and highlights engineering strategies that can be broadly applied to enhance the performance of protein-based VLP vaccines.
History
DepositionOct 4, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55303.png

Downloads & links

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Map

FileDownload / File: emd_55303.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChimpSELS Addomer map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.14258933 - 0.27034613
Average (Standard dev.)0.0008861205 (±0.009610836)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: ChimpSELS Addomer half map1

Fileemd_55303_half_map_1.map
AnnotationChimpSELS Addomer half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: ChimpSELS Addomer half map2

Fileemd_55303_half_map_2.map
AnnotationChimpSELS Addomer half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Adenovirus dodecahedron

EntireName: Adenovirus dodecahedron
Components
  • Complex: Adenovirus dodecahedron
    • Protein or peptide: Penton protein
  • Ligand: POTASSIUM ION

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Supramolecule #1: Adenovirus dodecahedron

SupramoleculeName: Adenovirus dodecahedron / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 3.65 MDa

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Macromolecule #1: Penton protein

MacromoleculeName: Penton protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Chimpanzee adenovirus Y25
Molecular weightTheoretical: 60.838066 KDa
Recombinant expressionOrganism: unidentified baculovirus
SequenceString: MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELSPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEFMYSNKF KARVMVSRKT PNGEFVTVTD G PGSQDILE ...String:
MMRRAYPEGP PPSYESVMQQ AMAAAAAMQP PLEAPYVPPR YLAPTEGRNS IRYSELSPLY DTTRLYLVDN KSADIASLNY QNDHSNFLT TVVQNNDFTP TEASTQTINF DERSRWGGQL KTIMHTNMPN VNEFMYSNKF KARVMVSRKT PNGEFVTVTD G PGSQDILE YEWVEFELPE GNFSVTMTID LMNNAIIDNY LAVGRQNGVL ESDIGVKFDT RNFRLGWDPV TELVMPGVYT NE AFHPDIV LLPGCGVDFT ESRLSNLLGI RKRQPFQEGF QIMYEDLEGG NIPALLDVDA YEKSKEESAA AARTAAVATA STE VDVRGD NFASPAAELV AAAEAAETES SRKIVIQPVE KDSKDRSYNV LPDKINTAYR SWYLAYNYGD PEKGVRSWTL LTTS DVTCG VEQVYWSLPD MMQDPVTFRS TRQVSNYPVV GAELLPVYSK SFFNEQAVYS QQLRAFTSLT HVFNRFPENQ ILVRP PAPT ITTVSENVPA LTDHGTLPLR SSIRGVQRVT VTDARRRTCP YVYKALGIVA PRVLSSRTF

UniProtKB: Penton protein

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Macromolecule #2: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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
GridMaterial: COPPER
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 44.01 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 147098
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9swa:
Adenovirus dodecahedron

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