9G3J

Circularly permuted lumazine synthase twisted tube with 28 Angstrom gap between double strands

This is a non-PDB format compatible entry.

Summary for 9G3J

• Entry DOI: 10.2210/pdb9g3j/pdb
• EMDB information: 51001
• Descriptor: 6,7-dimethyl-8-ribityllumazine synthase (1 entity in total)
• Functional Keywords: protein cage, protein engineering, self-assembly, geometry, helical reconstruction, bionanotechnology, polymorphism, pentamer, de novo protein
• Biological source: Aquifex aeolicus VF5; More
• Total number of polymer chains: 100
• Total formula weight: 1746593.40

Authors

Koziej, L.,Azuma, Y. (deposition date: 2024-07-12, release date: 2025-03-05, Last modification date: 2025-03-19)

Primary citation

Koziej, L.,Fatehi, F.,Aleksejczuk, M.,Byrne, M.J.,Heddle, J.G.,Twarock, R.,Azuma, Y.
Dynamic Assembly of Pentamer-Based Protein Nanotubes.
Acs Nano, 19:8786-8798, 2025

PubMed Abstract: Hollow proteinaceous particles are useful nanometric containers for delivery and catalysis. Understanding the molecular mechanisms and the geometrical theory behind the polymorphic protein assemblies provides a basis for designing ones with the desired morphology. As such, we found that a circularly permuted variant of a cage-forming enzyme, lumazine synthase, cpAaLS, assembles into a variety of hollow spherical and cylindrical structures in response to changes in ionic strength. Cryogenic electron microscopy revealed that these structures are composed entirely of pentameric subunits, and the dramatic cage-to-tube transformation is attributed to the moderately hindered 3-fold symmetry interaction and the imparted torsion angle of the building blocks, where both mechanisms are mediated by an α-helix domain that is untethered from the native position by circular permutation. Mathematical modeling suggests that the unique double- and triple-stranded helical arrangements of subunits are optimal tiling patterns, while different geometries should be possible by modulating the interaction angles of the pentagons. These structural insights into dynamic, pentamer-based protein cages and nanotubes afford guidelines for designing nanoarchitectures with customized morphology and assembly characteristics.

PubMed: 39993171
DOI: 10.1021/acsnano.4c16192

Experimental method

ELECTRON MICROSCOPY (3.1 Å)