8TAC

Designed DNA binding protein

8TAC の概要

• エントリーDOI: 10.2210/pdb8tac/pdb
• 分子名称: DBP48, DNA (5'-D(*AP*CP*CP*TP*GP*AP*CP*GP*CP*GP*A)-3'), DNA (5'-D(*TP*TP*CP*GP*CP*GP*TP*CP*AP*GP*GP)-3'), ... (4 entities in total)
• 機能のキーワード: dna binding, computational design, protein-dna complex, docking, de novo protein, de novo protein-dna complex, de novo protein/dna
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 22202.23

構造登録者

Doyle, L.,Stoddard, B.L.,Glasscock, C.J.,McHugh, R.P.,Pecoraro, R.J. (登録日: 2023-06-27, 公開日: 2024-08-28, 最終更新日: 2025-09-24)

主引用文献

Glasscock, C.J.,Pecoraro, R.J.,McHugh, R.,Doyle, L.A.,Chen, W.,Boivin, O.,Lonnquist, B.,Na, E.,Politanska, Y.,Haddox, H.K.,Cox, D.,Norn, C.,Coventry, B.,Goreshnik, I.,Vafeados, D.,Lee, G.R.,Gordan, R.,Stoddard, B.L.,DiMaio, F.,Baker, D.
Computational design of sequence-specific DNA-binding proteins.
Nat.Struct.Mol.Biol., 2025

PubMed Abstract: Sequence-specific DNA-binding proteins (DBPs) have critical roles in biology and biotechnology and there has been considerable interest in the engineering of DBPs with new or altered specificities for genome editing and other applications. While there has been some success in reprogramming naturally occurring DBPs using selection methods, the computational design of new DBPs that recognize arbitrary target sites remains an outstanding challenge. We describe a computational method for the design of small DBPs that recognize short specific target sequences through interactions with bases in the major groove and use this method to generate binders for five distinct DNA targets with mid-nanomolar to high-nanomolar affinities. The individual binding modules have specificity closely matching the computational models at as many as six base-pair positions and higher-order specificity can be achieved by rigidly positioning the binders along the DNA double helix using RFdiffusion. The crystal structure of a designed DBP-target site complex is in close agreement with the design model and the designed DBPs function in both Escherichia coli and mammalian cells to repress and activate transcription of neighboring genes. Our method provides a route to small and, hence, readily deliverable sequence-specific DBPs for gene regulation and editing.

PubMed: 40940539
DOI: 10.1038/s41594-025-01669-4

実験手法

X-RAY DIFFRACTION (2.34 Å)