9WHX

Cryo-EM structure of the IS621 recombinase in complex with bridge RNA, left-half DNA, and right-half DNA in the pre-strand exchange state

Summary for 9WHX

• Entry DOI: 10.2210/pdb9whx/pdb
• EMDB information: 65978
• Descriptor: IS621 transposase, bridge RNA, LH, top strand, ... (8 entities in total)
• Functional Keywords: holliday junction, rna dependent recombinase, recombination-dna-rna complex, dna binding protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 10
• Total formula weight: 312788.25

Authors

Hiraizumi, M.,Tsujimoto, E.,Shiojiri, N.,Nagahata, N.,Yamashita, K.,Nishimasu, H. (deposition date: 2025-08-27, release date: 2026-08-12, Last modification date: 2026-08-26)

Primary citation

Hiraizumi, M.,Athukoralage, J.S.,Perry, N.T.,Tsujimoto, E.,Shiojiri, N.,Nagahata, N.,Lee, L.,Sun, G.,Durrant, M.G.,Chandrasekaran, S.S.,Konermann, S.,Yamashita, K.,Hsu, P.D.,Nishimasu, H.
Structural mechanism governing the directionality of bridge recombination.
Nature, 2026

PubMed Abstract: Bridge recombinases from the IS110 family of transposons, such as IS621, associate with a bridge RNA (bRNA) to mediate programmable recombination between donor DNA and target DNA. Although insertion is mediated by the recombinase-bRNA complex, it remains unknown how IS621 elements are excised from host genomes to form the circular DNA intermediates required for transposition. Here we show that bRNA is weakly expressed from IS621 loci in the Escherichia coli genome and that the IS621 recombinase-bRNA complex mediates excision less efficiently than insertion. Furthermore, we present the cryo-electron microscopy structures of the IS621 recombinase-bRNA complex bound to excision DNA substrates, providing mechanistic insights into the excision reaction. Similar to the previously reported donor- and target-bound insertion complex, the excision complex comprises two recombinase dimers, each accommodating the target- and donor-binding loops of the bRNA. However, DNA recognition differs notably between the two complexes. Although the donor and target DNAs form a bent U-shape during insertion, the excision substrates adopt linear conformations and bind across both bRNA loops, forming an X-shaped structure. This geometry reduces the efficiency of top-strand exchange and contributes to the naturally observed bias favouring insertion over excision. Despite these differences, the efficiencies of both reactions are similarly modulated by base pairing between specific dinucleotides in the bRNA, termed handshake guides, and the top strands of the DNA substrates. Overall, this study provides mechanistic insights into the complete IS110 transposition cycle and facilitates the optimal design of programmable bridge-editing applications.

PubMed: 42587149
DOI: 10.1038/s41586-026-10903-y

Experimental method

ELECTRON MICROSCOPY (2.5 Å)