SNAP annotations: PDB entry 6cik

PDB-id

6cik; DSSR-derived features in text and JSON formats; DNAproDB

Class

recombination-DNA

Method

X-ray (3.15 Å)

Summary

Pre-reaction complex, rag1(e962q)-2-intact-nicked 12-23rss complex in mn2+

Reference

Kim MS, Chuenchor W, Chen X, Cui Y, Zhang X, Zhou ZH, Gellert M, Yang W (2018): "Cracking the DNA Code for V(D)J Recombination." Mol. Cell, 70, 358-370.e4. doi: 10.1016/j.molcel.2018.03.008.

Abstract

To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking.