9VMA

Cryo-EM structure of substrate-bound DRT9 hexamer complex

Summary for 9VMA

• Entry DOI: 10.2210/pdb9vma/pdb
• EMDB information: 65181
• Descriptor: RNA-dependent DNA polymerase, RNA (188-MER), DNA (5'-D(P*AP*AP*AP*A)-3'), ... (5 entities in total)
• Functional Keywords: complex, antiviral protein/rna/dna, antiviral protein-rna-dna complex
• Biological source: Escherichia coli; More
• Total number of polymer chains: 18
• Total formula weight: 722568.08

Authors

Zhang, S.,Zhang, H. (deposition date: 2025-06-27, release date: 2025-08-20, Last modification date: 2025-10-15)

Primary citation

Han, J.,Liu, B.,Tang, J.,Zhang, S.,Wang, X.,Li, X.,Zhang, Q.,Liu, Z.,Wang, W.,Liu, Y.,Zhou, R.,Yin, H.,Wei, Y.,Li, Z.,Zhang, M.,Deng, Z.,Zhang, H.
Non-coding RNA mediates the defense-associated reverse transcriptase (DRT) anti-phage oligomerization transition.
Embo J., 44:5429-5442, 2025

PubMed Abstract: Defense-associated reverse transcriptase (DRT) systems are implicated in prokaryotic resistance to viral infections, yet the molecular mechanisms underlying their functionality remain largely unknown. Here, we characterize a two-component DRT9 system, composed of a reverse transcriptase (RT) and a non-coding RNA (ncRNA), which exhibits a protein-primed DNA synthesis activity upon phage infection. We also determine its cryo-electron microscopy (cryo-EM) structures in different functional states. DRT9 RT binds to ncRNA, forming a dimer of dimers configuration that assembles into a trimer of dimers upon substrate binding. This oligomerization transition, crucial for DRT9-mediated anti-phage defense, is facilitated by a ncRNA cooperative self-assembly manner. Furthermore, substrate binding induces large conformational movements around the catalytic pocket of DRT9 RT, revealing a "lock-switch" mechanism for enzymatic activation. Notably, phylogenetic analysis and functional assays identify a unique N-terminal helix extension required for ncRNA stabilization and enzymatic activity, distinct from previously reported reverse transcriptase systems. Overall, our findings illuminate the molecular basis of DRT9-mediated antiviral defense and expand the functional and mechanistic diversity of the DRT family.

PubMed: 40836036
DOI: 10.1038/s44318-025-00544-8

Experimental method

ELECTRON MICROSCOPY (3.46 Å)