6VFJ | pdb_00006vfj

De novo designed icosahedral nanoparticle I53_dn5

• PDB DOI: https://doi.org/10.2210/pdb6VFJ/pdb
• EM Map EMD-21174: EMDB EMDataResource

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-05 Released: 2020-08-12 
• Deposition Author(s): Antanasijevic, A., Ward, A.B.
• Funding Organization(s): Bill & Melinda Gates Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Tailored design of protein nanoparticle scaffolds for multivalent presentation of viral glycoprotein antigens.

Ueda, G., Antanasijevic, A., Fallas, J.A., Sheffler, W., Copps, J., Ellis, D., Hutchinson, G.B., Moyer, A., Yasmeen, A., Tsybovsky, Y., Park, Y.J., Bick, M.J., Sankaran, B., Gillespie, R.A., Brouwer, P.J., Zwart, P.H., Veesler, D., Kanekiyo, M., Graham, B.S., Sanders, R.W., Moore, J.P., Klasse, P.J., Ward, A.B., King, N.P., Baker, D.

(2020) Elife 9

• PubMed: 32748788 
• DOI: https://doi.org/10.7554/eLife.57659
• Primary Citation Related Structures: 
  6V8E, 6VEH, 6VFH, 6VFI, 6VFJ


• PubMed Abstract: 
  

  Multivalent presentation of viral glycoproteins can substantially increase the elicitation of antigen-specific antibodies. To enable a new generation of anti-viral vaccines, we designed self-assembling protein nanoparticles with geometries tailored to present the ectodomains of influenza, HIV, and RSV viral glycoprotein trimers. We first de novo designed trimers tailored for antigen fusion, featuring N-terminal helices positioned to match the C termini of the viral glycoproteins. Trimers that experimentally adopted their designed configurations were incorporated as components of tetrahedral, octahedral, and icosahedral nanoparticles, which were characterized by cryo-electron microscopy and assessed for their ability to present viral glycoproteins. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles presented antigenically intact prefusion HIV-1 Env, influenza hemagglutinin, and RSV F trimers in the predicted geometries. This work demonstrates that antigen-displaying protein nanoparticles can be designed from scratch, and provides a systematic way to investigate the influence of antigen presentation geometry on the immune response to vaccination.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, United States.
Institute for Protein Design, University of Washington, Seattle, United States.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, United States.
International AIDS Vaccine Initiative Neutralizing Antibody Center, the Collaboration for AIDS Vaccine Discovery (CAVD) and Scripps Consortium for HIV/AIDS Vaccine Development (CHAVD), The Scripps Research Institute, La Jolla, United States.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States.
Department of Microbiology and Immunology, Weill Cornell Medicine, Cornell University, New York, United States.
Electron Microscopy Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, United States.
Berkeley Center for Structural Biology, Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley Laboratory, Berkeley, United States.
Amsterdam UMC, Department of Medical Microbiology, Amsterdam Infection & Immunity Institute, University of Amsterdam, Amsterdam, Netherlands.
Center for Advanced Mathematics in Energy Research Applications, Computational Research Division, Lawrence Berkeley Laboratory, Berkeley, United States.
Howard Hughes Medical Institute, University of Washington, Seattle, United States.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 120-mer - A60B60 

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

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 32.57 kDa 
• Atom Count: 2,196 
• Modeled Residue Count: 272 
• Deposited Residue Count: 283 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
I53_dn5B	A [auth B]	128	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
I53_dn5A	B [auth A]	155	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.35 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	Rosetta

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-12 
Deposition Author(s): Antanasijevic, A., Ward, A.B.

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Funding Organization	Location	Grant Number
Bill & Melinda Gates Foundation	United States	OPP1115782

Revision History  

• Version 1.0: 2020-08-12
  Type: Initial release
  
• Version 1.1: 2020-08-19
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references, Derived calculations