6V8E

Computationally designed C3-symmetric homotrimer from TPR repeat protein

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

  • Deposited: 2019-12-10 Released: 2020-08-12 
  • Deposition Author(s): Sankaran, B., Ueda, G., Zwart, P.H., Baker, D.
  • Funding Organization(s): Bill & Melinda Gates Foundation, National Science Foundation (NSF, United States), National Institutes of Health/Office of the Director, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
Designed protein
A, B, C, D, E
A, B, C, D, E, F
119synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.47α = 90
b = 64.91β = 106.33
c = 99.03γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1120319, OPP11157823, OPP1156262, OPP1115782, OPP1084519
National Science Foundation (NSF, United States)United StatesNSF CHE 1629214
National Institutes of Health/Office of the DirectorUnited StatesP41 GM103403-10
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169
Department of Energy (DOE, United States)United StatesDE-AC02-05CH11231

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, Structure summary
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.3: 2024-04-03
    Changes: Refinement description