6DBX

Cryo-EM structure of RAG in complex with 12-RSS substrate DNA

6DBX の概要

• エントリーDOI: 10.2210/pdb6dbx/pdb
• 関連するPDBエントリー: 6DBI 6DBJ 6DBL 6DBO 6DBQ 6DBR 6DBU 6DBV 6DBW 6DBX
• EMDBエントリー: 7843 7844 7845 7846 7847 7848 7849 7850 7851 7852 7853
• 分子名称: Recombination activating gene 1 - MBP chimera, Recombination activating gene 2, Forward strand of 12-RSS substrate DNA, ... (6 entities in total)
• 機能のキーワード: v(d)j recombination, rag complex, unmelted rss substrate, pre-cleveage complex, singly bound complex, recombination-dna complex, recombination/dna
• 由来する生物種: Escherichia coli; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 412287.84

構造登録者

Wu, H.,Liao, M.,Ru, H.,Mi, W. (登録日: 2018-05-03, 公開日: 2018-08-01, 最終更新日: 2024-03-13)

主引用文献

Ru, H.,Mi, W.,Zhang, P.,Alt, F.W.,Schatz, D.G.,Liao, M.,Wu, H.
DNA melting initiates the RAG catalytic pathway.
Nat. Struct. Mol. Biol., 25:732-742, 2018

PubMed Abstract: The mechanism for initiating DNA cleavage by DDE-family enzymes, including the RAG endonuclease, which initiates V(D)J recombination, is not well understood. Here we report six cryo-EM structures of zebrafish RAG in complex with one or two intact recombination signal sequences (RSSs), at up to 3.9-Å resolution. Unexpectedly, these structures reveal DNA melting at the heptamer of the RSSs, thus resulting in a corkscrew-like rotation of coding-flank DNA and the positioning of the scissile phosphate in the active site. Substrate binding is associated with dimer opening and a piston-like movement in RAG1, first outward to accommodate unmelted DNA and then inward to wedge melted DNA. These precleavage complexes show limited base-specific contacts of RAG at the conserved terminal CAC/GTG sequence of the heptamer, thus suggesting conservation based on a propensity to unwind. CA and TG overwhelmingly dominate terminal sequences in transposons and retrotransposons, thereby implicating a universal mechanism for DNA melting during the initiation of retroviral integration and DNA transposition.

PubMed: 30061602
DOI: 10.1038/s41594-018-0098-5

実験手法

ELECTRON MICROSCOPY (4.2 Å)