8FLX | pdb_00008flx

De novo designed homotrimer; the fusion product of BGL17 and DHR59


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 
    0.344 (Depositor), 0.350 (DCC) 
  • R-Value Work: 
    0.302 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 
    0.306 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Four-component protein nanocages designed by programmed symmetry breaking.

Lee, S.Kibler, R.D.Ahn, G.Hsia, Y.Borst, A.J.Philomin, A.Kennedy, M.A.Huang, B.Stoddard, B.Baker, D.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07814-1
  • Primary Citation of Related Structures:  
    8FLX

  • PubMed Abstract: 

    Four, eight or twenty C3 symmetric protein trimers can be arranged with tetrahedral, octahedral or icosahedral point group symmetry to generate closed cage-like structures 1,2 . Viruses access more complex higher triangulation number icosahedral architectures by breaking perfect point group symmetry 3-9 , but nature appears not to have explored similar symmetry breaking for tetrahedral or octahedral symmetries. Here we describe a general design strategy for building higher triangulation number architectures starting from regular polyhedra through pseudosymmetrization of trimeric building blocks. Electron microscopy confirms the structures of T = 4 cages with 48 (tetrahedral), 96 (octahedral) and 240 (icosahedral) subunits, each with 4 distinct chains and 6 different protein-protein interfaces, and diameters of 33 nm, 43 nm and 75 nm, respectively. Higher triangulation number viruses possess very sophisticated functionalities; our general route to higher triangulation number nanocages should similarly enable a next generation of multiple antigen-displaying vaccine candidates 10,11 and targeted delivery vehicles 12,13 .


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LK031352synthetic 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: 4.50 Å
  • R-Value Free:  0.344 (Depositor), 0.350 (DCC) 
  • R-Value Work:  0.302 (Depositor), 0.300 (DCC) 
  • R-Value Observed: 0.306 (Depositor) 
Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.477α = 90
b = 153.477β = 90
c = 153.477γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateMacCoss Yeast P41
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States5P41GM103533
National Science Foundation (NSF, United States)United StatesDGE-1762114
Other privateAudacious Project philanthropic funds
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM105691
Other government1S10D028581-01

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-28
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Data collection
  • Version 1.2: 2024-12-25
    Changes: Database references, Structure summary
  • Version 1.3: 2025-01-01
    Changes: Database references