5IM5

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.699 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/science.aaf8818
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Designed Riboflavin synthase
K, M, O, Q, S, A, B, C, D, E, F, G, H, I, J
156Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 11 
Gene Names: ribC
EC: 2.5.1.9
Find proteins for Q58584 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58584
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
P, T, N, V, W, U, Y, Z, X, 2, 4, 1, L, R, 3
219Vibrionales bacterium (strain SWAT-3)Mutation(s): 6 
EC: 4.1.3.16
Find proteins for A5KUH7 (Vibrionales bacterium (strain SWAT-3))
Go to UniProtKB:  A5KUH7
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.699 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.240 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 265.620α = 90.00
b = 279.810β = 90.00
c = 301.330γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Type: Database references