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. Author manuscript; available in PMC: 2018 Jun 5.
Published in final edited form as: Mol Cell. 2018 Apr 5;70(2):358–370.e4. doi: 10.1016/j.molcel.2018.03.008

Figure 5.

Figure 5

Coding flank recognition. A, B. Coding flanks in the PRC (A) and HFC (B) are bound by RAG1-C (blue) and RAG2 (pink) in the same Y-arm. The coding flank in the HFC is rotated by ∼180° and translocated by ∼ 8Å compared to the PRC, driven by the movement of ZnH2 and RAG2. 23RSS DNA, RAG1-C and RAG2-D are shown after superimposing RAG2-Ds. R848 is buried in the minor groove in the PRC (A), but interacts extensively with the beginning of the hairpin forming coding flank (CF-1) nucleotides in the major groove in the HFC. (B). Both CF-1 and one CF-9 are shown as sticks for reference. C. Superimposed structures of PRC and HFC reveal that the same protein surface contacts the major groove in the HFC (orange) and the widened minor groove in the PRC (yellow-orange). D. Fluorescence anisotropy-based DNA-binding analysis of RAG1/2. RAG1/2 binds intact and nicked 12- and 23-RSS DNAs equally well, but binds about 20-fold weaker to the hairpin product.