6VFJ

De novo designed icosahedral nanoparticle I53_dn5


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.7554/eLife.57659
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
I53_dn5BA [auth B]128synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
I53_dn5AB [auth A]155synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.0
MODEL REFINEMENTRosetta

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1115782

Revision History  (Full details and data files)

  • 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