9LP9

The cryo-EM structure of retron Eco8 in a standby state

Summary for 9LP9

• Entry DOI: 10.2210/pdb9lp9/pdb
• EMDB information: 63268
• Descriptor: Retron Eco8 OLD nuclease, Retron Eco8 reverse transcriptase, RNA (161-MER), ... (4 entities in total)
• Functional Keywords: retron, multi-copy single-stranded dna, eco8, anti-phage defense, old-family endonuclease, reverse transcriptase, antitoxin/dna/rna, antitoxin-dna-rna complex
• Biological source: Escherichia coli; More
• Total number of polymer chains: 16
• Total formula weight: 821917.48

Authors

Yuan, L.,Feng, Y. (deposition date: 2025-01-24, release date: 2025-11-19, Last modification date: 2025-12-03)

Primary citation

Yuan, L.,Xu, L.,Wu, B.,Liu, Q.,Yao, Y.,Hua, X.,Feng, Y.
Molecular mechanism of Eco8-mediated anti-phage defense.
Mol.Cell, 85:4229-4242.e4, 2025

PubMed Abstract: Escherichia coli Eco8 is an anti-phage defense system consisting of a reverse transcriptase, a class 3 overcoming lysogenization defect (OLD) nuclease, and a DNA-RNA chimera called multi-copy single-stranded DNA (msDNA). Genetic and biochemical data suggest that Eco8-mediated anti-phage defense is triggered by the phage single-stranded DNA (ssDNA)-binding proteins, but the underlying structural basis remains unknown. Here, we demonstrate that the DNA cleavage and ATP hydrolysis activities of the OLD nuclease are critical for Eco8-mediated anti-phage defense. We also determine the cryoelectron microscopy (cryo-EM) structures of Eco8 alone and in complex with the T7 phage ssDNA-binding protein. Structural analysis reveals that the reverse transcriptase, msDNA, and OLD nuclease form a megacomplex with a 4:4:4 stoichiometry. The T7 phage ssDNA-binding protein unwinds the msDNA and transforms Eco8 into an ATP-dependent DNA-degrading machinery. This study not only elucidates the molecular mechanism of Eco8-mediated anti-phage defense but also validates that msDNA serves as a sensor of phage DNA-modifying/binding proteins.

PubMed: 41172990
DOI: 10.1016/j.molcel.2025.09.029

Experimental method

ELECTRON MICROSCOPY (3.2 Å)