8F25 | pdb_00008f25

Cryo-EM structure of Lumazine synthase nanoparticle linked to VP8* antigen

• PDB DOI: https://doi.org/10.2210/pdb8F25/pdb
• EM Map EMD-28807: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Aquifex aeolicus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2022-11-07 Released: 2023-04-12 
• Deposition Author(s): Mangala Prasad, V., Lee, K.K.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

mRNA-based VP8* nanoparticle vaccines against rotavirus are highly immunogenic in rodents.

Roier, S., Mangala Prasad, V., McNeal, M.M., Lee, K.K., Petsch, B., Rauch, S.

(2023) NPJ Vaccines 8: 190-190

• PubMed: 38129390 
• DOI: https://doi.org/10.1038/s41541-023-00790-z
• Primary Citation Related Structures: 
  8F25


• PubMed Abstract: 
  

  Despite the availability of live-attenuated oral vaccines, rotavirus remains a major cause of severe childhood diarrhea worldwide. Due to the growing demand for parenteral rotavirus vaccines, we developed mRNA-based vaccine candidates targeting the viral spike protein VP8*. Our monomeric P2 (universal T cell epitope)-VP8* mRNA design is equivalent to a protein vaccine currently in clinical development, while LS (lumazine synthase)-P2-VP8* was designed to form nanoparticles. Cyro-electron microscopy and western blotting-based data presented here suggest that proteins derived from LS-P2-VP8* mRNA are secreted in vitro and self-assemble into 60-mer nanoparticles displaying VP8*. mRNA encoded VP8* was immunogenic in rodents and introduced both humoral and cellular responses. LS-P2-VP8* induced superior humoral responses to P2-VP8* in guinea pigs, both as monovalent and trivalent vaccines, with encouraging responses detected against the most prevalent P genotypes. Overall, our data provide evidence that trivalent LS-P2-VP8* represents a promising mRNA-based next-generation rotavirus vaccine candidate.

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Organizational Affiliation: 
• CureVac SE, Tübingen, Germany.
Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
Department of Pediatrics, University of Cincinnati College of Medicine, Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
CureVac SE, Tübingen, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 1,003.69 kDa 
• Atom Count: 70,560 
• Modeled Residue Count: 9,240 
• Deposited Residue Count: 9,240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, AA [auth 0], AB [auth q], B, BA [auth 1], BB [auth r], C, CA [auth 2], CB [auth s], D, DA [auth 3], DB [auth t], E, EA [auth 4], EB [auth u], F, FA [auth 5], FB [auth v], G, GA [auth 6], GB [auth w], H, HA [auth 7], HB [auth x], I, IA [auth 8], J, JA [auth 9], K, KA [auth a], L, LA [auth b], M, MA [auth c], N, NA [auth d], O, OA [auth e], P, PA [auth f], Q, QA [auth g], R, RA [auth h], S, SA [auth i], T, TA [auth j], U, UA [auth k], V, VA [auth l], W, WA [auth m], X, XA [auth n], Y, YA [auth o], Z, ZA [auth p]	154	Aquifex aeolicus	Mutation(s): 0  Gene Names: ribH, aq_132 EC: 2.5.1.78
UniProt
Find proteins for O66529 (Aquifex aeolicus (strain VF5)) Explore O66529  Go to UniProtKB:  O66529

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-04-12 
Deposition Author(s): Mangala Prasad, V., Lee, K.K.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	--

Revision History  

• Version 1.0: 2023-04-12
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references