9DRL

Cryo-EM structure of the T33-549 tetrahedral cage

This is a non-PDB format compatible entry.

Summary for 9DRL

• Entry DOI: 10.2210/pdb9drl/pdb
• EMDB information: 47128
• Descriptor: T33-549_B, T33-549_A (2 entities in total)
• Functional Keywords: nanomaterial, protein cages, de novo protein
• Biological source: synthetic construct; More
• Total number of polymer chains: 24
• Total formula weight: 1190801.40

Authors

Redler, R.,Coudray, N.,Lubner, J.,Wang, S.,Baker, D.,Ekiert, D.C.,Bhabha, G. (deposition date: 2024-09-25, release date: 2025-08-06, Last modification date: 2025-10-15)

Primary citation

Wang, S.,Favor, A.,Kibler, R.D.,Lubner, J.M.,Borst, A.J.,Coudray, N.,Redler, R.L.,Chiang, H.T.,Sheffler, W.,Hsia, Y.,Bethel, N.P.,Li, Z.,Ekiert, D.C.,Bhabha, G.,Pozzo, L.D.,Baker, D.
Bond-centric modular design of protein assemblies.
Nat Mater, 24:1644-1652, 2025

PubMed Abstract: Directional interactions that generate regular coordination geometries are a powerful means of guiding molecular and colloidal self-assembly, but implementing such high-level interactions with proteins remains challenging due to their complex shapes and intricate interface properties. Here we describe a modular approach to protein nanomaterial design inspired by the rich chemical diversity that can be generated from the small number of atomic valencies. We design protein building blocks using deep learning-based generative tools, incorporating regular coordination geometries and tailorable bonding interactions that enable the assembly of diverse closed and open architectures guided by simple geometric principles. Experimental characterization confirms the successful formation of more than 20 multicomponent polyhedral protein cages, two-dimensional arrays and three-dimensional protein lattices, with a high (10%-50%) success rate and electron microscopy data closely matching the corresponding design models. Due to modularity, individual building blocks can assemble with different partners to generate distinct regular assemblies, resulting in an economy of parts and enabling the construction of reconfigurable networks for designer nanomaterials.

PubMed: 40745093
DOI: 10.1038/s41563-025-02297-5

Experimental method

ELECTRON MICROSCOPY (6.1 Å)