9Y66

attLsym bound serine integrase complex in the dimeric state

Summary for 9Y66

• Entry DOI: 10.2210/pdb9y66/pdb
• Related: 9DXD 9DXF 9DXG 9DXH 9DXJ 9DXK
• EMDB information: 72552
• Descriptor: Site-specific recombinase, attLsym, ZINC ION, ... (4 entities in total)
• Functional Keywords: site-specific dna recombinase, large serine integrase, dna binding domains, recombinase, resolvase, zinc ribbon recombinase, recombination
• Biological source: Spbetavirus SPbeta; More
• Total number of polymer chains: 4
• Total formula weight: 165418.01

Authors

Shin, H.,Pigli, Y.,Pena Reyes, T.,Fuller, J.R.,Olorunniji, F.J.,Rice, P.A. (deposition date: 2025-09-08, release date: 2026-02-04)

Primary citation

Shin, H.,Pigli, Y.,Pena Reyes, T.,Fuller, J.R.,Olorunniji, F.J.,Rice, P.A.
Structural basis of directionality control in large serine integrases
Biorxiv, 2025

PubMed Abstract: Large serine integrases (LSIs) catalyze unidirectional site-specific DNA recombination reactions, yet those reactions are reversed by the presence of a cognate recombination directionality factor (RDF). Mechanistic understanding of directionality control has been hampered by a lack of structural information. Here, we use cryo-electron microscopy (cryo-EM) to determine the structures of six SPbeta integrase-DNA complexes along the integrative (-RDF) and excisive (+RDF) reaction pathways, at 4.16-7.18Å resolution. Our findings reveal how RDF-mediated repositioning of an integrase subdomain (1) dictates which pairs of DNA sites can be assembled into a synaptic complex to initiate recombination and (2) dictates which product complexes will be conformationally locked, preventing the back reaction. These mechanistic insights provide a conceptual framework for engineering efficient and versatile genome editing tools.

PubMed: 39803483
DOI: 10.1101/2025.01.03.631226

Experimental method

ELECTRON MICROSCOPY (3.31 Å)