6HCR | pdb_00006hcr

Synthetic Self-assembling ADDomer Platform for Highly Efficient Vaccination by Genetically-encoded Multi-epitope Display

• PDB DOI: https://doi.org/10.2210/pdb6HCR/pdb
• EM Map EMD-0198: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Human adenovirus B3
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-08-16 Released: 2019-08-28 
• Deposition Author(s): Bufton, J.C., Berger, I., Schaffitzel, C., Garzoni, F., Rabi, F.A.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display.

Vragniau, C., Bufton, J.C., Garzoni, F., Stermann, E., Rabi, F., Terrat, C., Guidetti, M., Josserand, V., Williams, M., Woods, C.J., Viedma, G., Bates, P., Verrier, B., Chaperot, L., Schaffitzel, C., Berger, I., Fender, P.

(2019) Sci Adv 5: eaaw2853-eaaw2853

• PubMed: 31620562 
• DOI: https://doi.org/10.1126/sciadv.aaw2853
• Primary Citation Related Structures: 
  6HCR


• PubMed Abstract: 
  

  Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein-based self-assembling nanoparticle scaffold engineered to facilitate plug-and-play display of multiple immunogenic epitopes from pathogens. We used cryo-electron microscopy at near-atomic resolution and implemented novel, cost-effective, high-performance cloud computing to reveal architectural features in unprecedented detail. We analyzed ADDomer interaction with components of the immune system and developed a promising first-in-kind ADDomer-based vaccine candidate to combat emerging Chikungunya infectious disease, exemplifying the potential of our approach.

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Organizational Affiliation: 
• Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042 Grenoble, France.
Bristol Research Centre for Synthetic Biology BrisSynBio, School of Biochemistry, University of Bristol, 1 Tankard's Close, Bristol BS8 1TD, UK.
Imophoron Ltd., Unit DX, St. Philips Central, Albert Road, Bristol BS2 OXJ, UK.
Laboratoire de Biologie Tissulaire et d'Ingénierie Thérapeutique (LBTI), UMR 5305, Université Lyon 1, CNRS, Institut de Biologie et Chimie des Protéines (IBCP), Lyon, France.
Cancer Target and Experimental Therapeutics, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, 38700 Grenoble, France.
Advanced Computing Research Centre, University of Bristol, 31 Great George Street, Bristol BS1 5QD, UK.
Oracle Cloud Development Centre, Tower Wharf, Cheese Lane, Bristol BS2 2JJ, UK.
Immunobiology and Immunotherapy in Chronic Diseases, Institute for Advanced Biosciences, INSERM U1209, CNRS UMR5309, Université Grenoble Alpes, Etablissement Français du Sang-Rhone-Alpes, 38700 Grenoble, France.
Max Planck-Bristol Centre for Minimal Biology, Cantock's Close, Bristol BS8 1TS, UK.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: equilibrium centrifugation, equilibrium centrifugation

Macromolecule Content 

• Total Structure Weight: 3,815.9 kDa 
• Atom Count: 213,720 
• Modeled Residue Count: 26,460 
• Deposited Residue Count: 33,540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penton protein	A [auth z], AA [auth a], AB [auth 2], B [auth A], BA [auth b], BB [auth 3], C [auth B], CA [auth c], CB [auth 4], D [auth C], DA [auth d], DB [auth 5], E [auth D], EA [auth e], EB [auth 6], F [auth E], FA [auth f], FB [auth 7], G [auth F], GA [auth g], GB [auth 8], H [auth G], HA [auth h], HB [auth 9], I [auth H], IA [auth i], J [auth I], JA [auth j], K [auth J], KA [auth k], L [auth K], LA [auth l], M [auth L], MA [auth m], N [auth M], NA [auth n], O [auth N], OA [auth o], P [auth O], PA [auth p], Q [auth P], QA [auth q], R [auth Q], RA [auth r], S [auth R], SA [auth s], T [auth S], TA [auth t], U [auth T], UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth 1]	559	Human adenovirus B3	Mutation(s): 0  Gene Names: L2
UniProt
Find proteins for Q2Y0H9 (Human adenovirus B serotype 3) Explore Q2Y0H9  Go to UniProtKB:  Q2Y0H9

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-28 
Deposition Author(s): Bufton, J.C., Berger, I., Schaffitzel, C., Garzoni, F., Rabi, F.A.

Revision History  

• Version 1.0: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-10-30
  Changes: Data collection, Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Refinement description