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- PDB-9swa: Adenovirus dodecahedron -

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Basic information

Entry
Database: PDB / ID: 9swa
TitleAdenovirus dodecahedron
ComponentsPenton protein
KeywordsVIRUS LIKE PARTICLE / adenovirus / 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
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsKabasakal, B.V. / Buzas, D. / Bufton, J. / Berger-Schaffitzel, C. / Berger, I.
Funding support United Kingdom, 3items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Penton protein
2: Penton protein
3: Penton protein
4: Penton protein
5: Penton protein
6: Penton protein
7: Penton protein
8: Penton protein
9: Penton protein
A: Penton protein
B: Penton protein
C: Penton protein
D: Penton protein
E: Penton protein
F: Penton protein
G: Penton protein
H: Penton protein
I: Penton protein
J: Penton protein
K: Penton protein
L: Penton protein
M: Penton protein
N: Penton protein
O: Penton protein
P: Penton protein
Q: Penton protein
R: Penton protein
S: Penton protein
T: Penton protein
V: Penton protein
W: Penton protein
X: Penton protein
Y: Penton protein
Z: Penton protein
a: Penton protein
b: Penton protein
c: Penton protein
d: Penton protein
e: Penton protein
f: Penton protein
g: Penton protein
h: Penton protein
i: Penton protein
j: Penton protein
k: Penton protein
l: Penton protein
m: Penton protein
n: Penton protein
o: Penton protein
p: Penton protein
q: Penton protein
r: Penton protein
s: Penton protein
t: Penton protein
u: Penton protein
v: Penton protein
w: Penton protein
x: Penton protein
y: Penton protein
z: Penton protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,650,75372
Polymers3,650,28460
Non-polymers46912
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Penton protein / CP-P / Penton base protein / Protein III


Mass: 60838.066 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chimpanzee adenovirus Y25 / Gene: L2 / Production host: unidentified baculovirus / References: UniProt: G9G849
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: K
Has ligand of interestN
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: Adenovirus dodecahedron / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 3.65 MDa / Experimental value: NO
Source (natural)Organism: Chimpanzee adenovirus Y25
Source (recombinant)Organism: unidentified baculovirus
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 44.01 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELIONparticle selection
4CTFFINDCTF correction
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
12RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147098 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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