9I2F

Cryo-EM structure of retron Eco2 (Ec67)

Summary for 9I2F

• Entry DOI: 10.2210/pdb9i2f/pdb
• Related: 9I2G 9S1F
• EMDB information: 52583
• Descriptor: msDNA (67-MER), Retron Ec67 protein, RNA (132-MER) (3 entities in total)
• Functional Keywords: retron, reverse transcriptase, dna, rna, toprim, rnaseh, msdna, antiviral protein
• Biological source: Escherichia coli NCTC 86; More
• Total number of polymer chains: 9
• Total formula weight: 394881.71

Authors

Jasnauskaite, M.,Miksys, A.,Skorupskaite, A.,Malinauskaite, L.,Pausch, P. (deposition date: 2025-01-20, release date: 2026-02-04, Last modification date: 2026-02-25)

Primary citation

Jasnauskaite, M.,Juozapaitis, J.,Liegute, T.,Grigaitis, R.,Skorupskaite, A.,Steinchen, W.,Miksys, A.,Truncaite, L.,Kazlauskaite, K.,Torres Jimenez, M.F.,Khochare, S.,Dudas, G.,Bange, G.,Malinauskaite, L.,Songailiene, I.,Pausch, P.
Structure and mechanism of antiphage retron Eco2.
Nat.Struct.Mol.Biol., 33:330-340, 2026

PubMed Abstract: Retrons are prokaryotic reverse transcriptase systems that produce multicopy single-stranded DNA (msDNA), yet the principles by which they mediate antiviral defense remain largely unresolved. Here we investigate the mechanism of Escherichia coli Eco2, a minimal retron composed of a single reverse transcriptase-nuclease fusion protein. Cryogenic electron microscopy and hydrogen/deuterium exchange mass spectrometry reveal the structures and dynamics of a trimeric nucleoprotein complex assembled within a branched msDNA scaffold, which cages the TOPRIM nucleases. We show that the phage-encoded endonuclease DenB initiates msDNA degradation, thereby unblocking the nuclease active sites. Activated Eco2 cuts transfer RNAs, resulting in translational shutdown for antiphage defense. We further identify ribosomal protein S1 as a putative RNA chaperone that associates with the msDNA precursor. These findings provide insights into the molecular mechanisms of minimal retrons and establish a structural basis for engineering of Eco2.

PubMed: 41709047
DOI: 10.1038/s41594-026-01754-2

Experimental method

ELECTRON MICROSCOPY (2.8 Å)