6CIK

Pre-Reaction Complex, RAG1(E962Q)/2-intact/nicked 12/23RSS complex in Mn2+

Summary for 6CIK

• Entry DOI: 10.2210/pdb6cik/pdb
• Related: 4WWX 5ZDZ 5ZE0 5ZE1 5ZE2 6CG0 6CIJ 6CIL 6CIM
• Descriptor: V(D)J recombination-activating protein 1, MANGANESE (II) ION, V(D)J recombination-activating protein 2, ... (11 entities in total)
• Functional Keywords: vdj recombination, rss, rag1/2, recombination, recombination-dna complex, recombination/dna
• Biological source: Mus musculus (Mouse); More
• Total number of polymer chains: 10
• Total formula weight: 300835.30

Authors

Chuenchor, W.,Chen, X.,Kim, M.S.,Gellert, M.,Yang, W. (deposition date: 2018-02-24, release date: 2018-04-25, Last modification date: 2023-10-04)

Primary citation

Kim, M.S.,Chuenchor, W.,Chen, X.,Cui, Y.,Zhang, X.,Zhou, Z.H.,Gellert, M.,Yang, W.
Cracking the DNA Code for V(D)J Recombination.
Mol. Cell, 70:358-370.e4, 2018

PubMed 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.

PubMed: 29628308
DOI: 10.1016/j.molcel.2018.03.008

Experimental method

X-RAY DIFFRACTION (3.15 Å)