5IM4 image
Deposition Date 2016-03-05
Release Date 2016-07-27
Last Version Date 2023-09-27
Entry Detail
PDB ID:
5IM4
Keywords:
Title:
Crystal structure of designed two-component self-assembling icosahedral cage I52-32
Biological Source:
Method Details:
Experimental Method:
Resolution:
3.50 Å
R-Value Free:
0.23
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
H 3
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:6,7-dimethyl-8-ribityllumazine synthase
Mutations:R29L, K30E, D33A, V40I, E50A
Chain IDs:A, B (auth: E), C, D (auth: B), E (auth: D), K, L, M (auth: N), N (auth: M), O, U, V, W (auth: X), X (auth: W), Y, EA (auth: e), FA (auth: f), GA (auth: h), HA (auth: g), IA (auth: i)
Chain Length:138
Number of Molecules:20
Biological Source:Candida albicans P37005
Polymer Type:polypeptide(L)
Molecule:Phosphotransferase system, mannose/fructose-specific component IIA
Gene (Uniprot):ManX
Mutations:V45K, R47A, E51M, K52R, K55I, E56A, Q59A, S81E, E85T, Y86F
Chain IDs:F, G (auth: H), H (auth: G), I, J, P, Q, R (auth: S), S (auth: R), T, Z (auth: b), AA (auth: d), BA (auth: c), CA (auth: Z), DA (auth: a), JA (auth: j), KA (auth: k), LA (auth: m), MA (auth: l), NA (auth: n)
Chain Length:138
Number of Molecules:20
Biological Source:Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)
Ligand Molecules
Primary Citation
Accurate design of megadalton-scale two-component icosahedral protein complexes.
Science 353 389 394 (2016)
PMID: 27463675 DOI: 10.1126/science.aaf8818

Abstact

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.

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Primary Citation of related structures