9LX4

Crystal structure of the de novo designed protein ZZ4

Summary for 9LX4

• Entry DOI: 10.2210/pdb9lx4/pdb
• Descriptor: ZZ4, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (3 entities in total)
• Functional Keywords: de novo protein
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 38427.87

Authors

Zhao, Z.,Hattori, M. (deposition date: 2025-02-17, release date: 2025-06-04, Last modification date: 2026-07-01)

Primary citation

Zhao, Z.,Omae, K.,Iwasaki, W.,Zhang, Z.,Pan, F.,Lee, E.J.,Ito, K.,Hattori, M.
Bioinformatics classification of the MgtE Mg 2 + channel and de novo protein design for the stabilization of its novel subclass.
Acta Biochim.Biophys.Sin., 58:1402-1412, 2026

PubMed Abstract: MgtE channels play crucial roles in Mg homeostasis and are implicated in bacterial survival under antibiotic exposure. Previous structural and biophysical studies have focused predominantly on MgtE, leaving the structural and mechanistic diversity of MgtE family proteins largely unexplored. In this study, via a genome mining approach, we identify diverse MgtE homologs, including a novel subclass termed the "mini-N type", which lacks the canonical cytoplasmic N and CBS domains but possesses a unique small N-like domain. Despite extensive expression screening, mini-N-type homologs cannot be stably purified. To address this issue, we design a series of proteins and determine their crystal structures. A selected protein is fused to a mini-N-type MgtE, enabling successful purification and preliminary cryo-EM imaging. Our findings demonstrate that -designed protein fusions serve as powerful tools for stabilizing and purifying otherwise unstable membrane proteins, opening new avenues for structural and functional studies of otherwise inaccessible membrane proteins.

PubMed: 42305050
DOI: 10.3724/abbs.2025224

Experimental method

X-RAY DIFFRACTION (2.03 Å)