9JPU

CryoEM structure of mouse RAG SEC-PHD

9JPU の概要

• エントリーDOI: 10.2210/pdb9jpu/pdb
• EMDBエントリー: 61715
• 分子名称: V(D)J recombination-activating protein 1, V(D)J recombination-activating protein 2, DNA (5'-D(P*GP*GP*CP*TP*GP*TP*AP*TP*CP*AP*CP*TP*GP*TP*G)-3'), ... (9 entities in total)
• 機能のキーワード: v(d)j recombination, rag, phd, transposition, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• 由来する生物種: Mus musculus (house mouse); 詳細
• タンパク質・核酸の鎖数: 9
• 化学式量合計: 434274.32

構造登録者

Chen, X.,Yao, L.,Yang, W.,Gellert, M. (登録日: 2024-09-26, 公開日: 2025-07-23, 最終更新日: 2026-02-04)

主引用文献

Chen, X.,Yao, L.,Li, W.,Ma, S.,Yuan, X.,Yang, Y.,Yuan, Y.,Liu, Y.,Liu, L.,Wang, H.,Gellert, M.,Yang, W.
How RAG1/2 evolved from ancestral transposases to initiate V(D)J recombination without transposition.
Proc.Natl.Acad.Sci.USA, 122:e2512362122-e2512362122, 2025

PubMed Abstract: The recombination activating genes 1 and 2 (RAG1/2) recombinase, which initiates V(D)J recombination in jawed vertebrates, evolved from RNaseH-like transposases such as Transib and ProtoRAG. However, its postcleavage transposase activity is strictly suppressed. Previous structural studies have focused only on the conserved core domains of RAG1/2, leaving the regulatory mechanisms of the noncore regions unclear. To investigate how RAG1/2 suppresses transposition and regulates DNA cleavage, we determined cryo-electron microscopy (cryo-EM) structures of nearly full-length RAG1/2 complexed with cleaved recombination signal sequences (RSS) in a signal-end complex (SEC) at resolutions up to 2.95 Å. Two key structures, SEC-0 and SEC-Plant Homeodomain (PHD), reveal distinct regulatory roles of RAG2, which is absent in Transib transposase. SEC-0 displays a closed conformation, revealing that the core RAG2 facilitates sequential DNA cleavage by stabilizing the RSS-cleaved states in a "spring-loaded" mechanism. SEC-PHD reveals how RAG2's noncore PHD and Acidic Hinge (AH), which are absent in ProtoRAG, inhibit target DNA binding in transposition. Histone H3K4me3, which recruits RAG1/2 to RSS sites, does not influence RAG1/2 binding to V, D, or J gene segments bordered by RSS. In contrast, the suppressed transposition can be activated by H3K4me3 peptides that dislodge the inhibitory PHD. To achieve this derepression in vivo, however, would require an unlikely close placement of two nucleosomes flanking a target DNA bent by nearly 180°. Our structural and biochemical results elucidate how RAG1 has acquired RAG2 and utilizes its core and noncore domains to enhance V(D)J recombination and suppress transposition.

PubMed: 40729386
DOI: 10.1073/pnas.2512362122

実験手法

ELECTRON MICROSCOPY (3.25 Å)