5IM5

Crystal structure of designed two-component self-assembling icosahedral cage I53-40


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Accurate design of megadalton-scale two-component icosahedral protein complexes.

Bale, J.B.Gonen, S.Liu, Y.Sheffler, W.Ellis, D.Thomas, C.Cascio, D.Yeates, T.O.Gonen, T.King, N.P.Baker, D.

(2016) Science 353: 389-394

  • DOI: https://doi.org/10.1126/science.aaf8818
  • Primary Citation of Related Structures:  
    5IM4, 5IM5, 5IM6

  • PubMed Abstract: 

    Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. Graduate Program in Molecular and Cellular Biology, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed Riboflavin synthase156Methanocaldococcus jannaschii DSM 2661Mutation(s): 11 
Gene Names: ribCMJ1184
EC: 2.5.1.9
UniProt
Find proteins for Q58584 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q58584 
Go to UniProtKB:  Q58584
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58584
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase219Vibrionales bacterium SWAT-3Mutation(s): 6 
Gene Names: VSWAT3_13722
EC: 4.1.3.16
UniProt
Find proteins for A5KUH7 (Vibrionales bacterium (strain SWAT-3))
Explore A5KUH7 
Go to UniProtKB:  A5KUH7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5KUH7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 265.62α = 90
b = 279.81β = 90
c = 301.33γ = 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: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description