9YFD

Defense-associated reverse transcriptase 1 (DRT1) filament

Summary for 9YFD

• Entry DOI: 10.2210/pdb9yfd/pdb
• EMDB information: 72883
• Descriptor: Defense-associated reverse transcriptase 1, 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: anti-phage defense, dna synthesis, nitrilase domain, rt domain, filament, antiviral protein
• Biological source: Escherichia coli
• Total number of polymer chains: 8
• Total formula weight: 1136734.21

Authors

Johnson, N.V.,McLellan, J.S. (deposition date: 2025-09-25, release date: 2026-06-03, Last modification date: 2026-07-01)

Primary citation

Neville, N.,Johnson, N.V.,Escobar, E.E.,Chiang, C.H.,Nreca, A.,Johnson, S.R.,Dai, N.,Hanneman, A.,Correa Jr., I.R.,McLellan, J.S.,Trachman 3rd, R.J.
Semirandom DNA adducts regulate a filamentous defense-associated reverse transcriptase.
Nat.Struct.Mol.Biol., 33:953-961, 2026

PubMed Abstract: Retrons and several defense-associated reverse transcriptases (DRTs) synthesize non-genomic DNA for bacteriophage immunity. In some instances, this non-genomic DNA is of undefined, semirandom sequence. How undefined DNA sequences impart antiphage defense is not known. Herewe report the cryo-EM structure and functional characterization of the DRT1 antiphage defense system. We show that DRT1 performs template-free, protein-primed DNA synthesis to generate semirandom DNA adducts. DNA synthesis activates the nitrilase domain of DRT1, while DNA adducts drive the assembly of quiescent DRT1 filaments. Filamentous DRT1 is composed of domain-swapped C termini that are entwined, forming pseudoknots between tetrameric stacks. This configuration occludes conserved active-site residues, resulting in a dormant state. Bacteriophage escape mutants identify a T4 single-stranded DNA helicase required for DRT1 activity. Functionally, DRT1 resembles a minimal retron where a single gene produces a reverse transcriptase, effector and non-genomic antitoxin DNA.

PubMed: 42271041
DOI: 10.1038/s41594-026-01813-8

Experimental method

ELECTRON MICROSCOPY (2.6 Å)