4NWR

Computationally Designed Two-Component Self-Assembling Tetrahedral Cage T33-28


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Accurate design of co-assembling multi-component protein nanomaterials.

King, N.P.Bale, J.B.Sheffler, W.McNamara, D.E.Gonen, S.Gonen, T.Yeates, T.O.Baker, D.

(2014) Nature 510: 103-108

  • DOI: https://doi.org/10.1038/nature13404
  • Primary Citation of Related Structures:  
    4NWN, 4NWO, 4NWP, 4NWQ, 4NWR

  • PubMed Abstract: 

    The self-assembly of proteins into highly ordered nanoscale architectures is a hallmark of biological systems. The sophisticated functions of these molecular machines have inspired the development of methods to engineer self-assembling protein nanostructures; however, the design of multi-component protein nanomaterials with high accuracy remains an outstanding challenge. Here we report a computational method for designing protein nanomaterials in which multiple copies of two distinct subunits co-assemble into a specific architecture. We use the method to design five 24-subunit cage-like protein nanomaterials in two distinct symmetric architectures and experimentally demonstrate that their structures are in close agreement with the computational design models. The accuracy of the method and the number and variety of two-component materials that it makes accessible suggest a route to the construction of functional protein nanomaterials tailored to specific applications.


  • Organizational Affiliation

    1] Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA [2] Institute for Protein Design, University of Washington, Seattle, Washington 98195, USA [3].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
integron gene cassette protein158uncultured bacteriumMutation(s): 10 
Gene Names: ORF1
UniProt
Find proteins for B0BGB0 (uncultured bacterium)
Explore B0BGB0 
Go to UniProtKB:  B0BGB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0BGB0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage migration inhibitory factor-like protein121Leishmania majorMutation(s): 8 
Gene Names: LMJF_33_1740MIF1
UniProt
Find proteins for Q4Q413 (Leishmania major)
Explore Q4Q413 
Go to UniProtKB:  Q4Q413
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4Q413
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.262 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.91α = 90
b = 189.25β = 90.02
c = 376.83γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-04
    Changes: Database references
  • Version 1.2: 2014-06-11
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Refinement description