5IM4

Crystal structure of designed two-component self-assembling icosahedral cage I52-32


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

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: 10.1126/science.aaf8818
  • Structures With Same Primary Citation

  • 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. Institute for Protein Design, University of Washington, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. neilking@uw.edu dabaker@uw.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6,7-dimethyl-8-ribityllumazine synthaseA, B, C, D, E, K, L, M, N, O, U, V, W, X, Y, e, f, g, h, i162Candida albicans P37005Mutation(s): 5 
Gene Names: MEU_00538
EC: 2.5.1.78
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Phosphotransferase system, mannose/fructose-specific component IIAF, G, H, I, J, P, Q, R, S, T, Z, a, b, c, d, j, k, l, m, n138Caldanaerobacter subterraneus subsp. tengcongensis MB4Mutation(s): 10 
Gene Names: ManXTTE0192
Find proteins for Q8RD55 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4))
Explore Q8RD55 
Go to UniProtKB:  Q8RD55
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 258.82α = 90
b = 258.82β = 90
c = 641.73γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-10
    Changes: Database references
  • Version 1.2: 2017-11-01
    Changes: Author supporting evidence, Database references, Derived calculations