9OM4

Cryo-EM structure of filament form Acidithiobacillus caldus (Aca) short prokaryotic argonautes, HNH-associated (SPARHA) with gRNA and tDNA

Summary for 9OM4

• Entry DOI: 10.2210/pdb9om4/pdb
• EMDB information: 70606
• Descriptor: HNH endonuclease, Prokaryotic argonaute MID-PIWI family protein, RNA (5'-R(P*AP*UP*UP*UP*GP*GP*UP*UP*GP*CP*GP*GP*UP*GP*CP*UP*CP*U)-3'), ... (5 entities in total)
• Functional Keywords: sparha, prokaryotic argonaute, nuclease, immune system, immune system-dna-rna complex, immune system/dna/rna
• Biological source: Acidithiobacillus caldus; More
• Total number of polymer chains: 16
• Total formula weight: 458707.44

Authors

Murakami, K.S.,Narwal, M. (deposition date: 2025-05-13, release date: 2025-10-22, Last modification date: 2026-05-13)

Primary citation

Kanevskaya, A.,Narwal, M.,Lisitskaya, L.,Moiseenko, A.V.,Sokolova, O.S.,Sluchanko, N.N.,Murakami, K.S.,Kulbachinskiy, A.
Argonaute-HNH filaments triggered by invader DNA confer bacterial immunity.
Nat Commun, 16:11389-11389, 2025

PubMed Abstract: Argonaute proteins provide innate immunity in all domains of life through guide-dependent recognition and cleavage of invader nucleic acids. Many short prokaryotic Argonautes (pAgos) lack nuclease activity and are instead co-encoded with tentative nuclease effectors, but their activation mechanisms remain unknown. Here, we characterize SPARHA systems (short prokaryotic argonautes, HNH-associated), containing HNH nuclease effectors. RNA-guided target DNA recognition by pAgo induces formation of SPARHA filaments with a chain of double nuclease sites formed by HNH tetramers, leading to indiscriminate collateral degradation of DNA and protecting bacterial population from invaders. We show that the assembly of filaments proceeds via a universal activation pathway involving a cascade of target-induced conformational changes in SPARHA, conserved in other short pAgo systems containing various types of effectors. pAgos and associated effectors act as modular defense systems that translate recognition of specific DNA into immune response through assembly of supramolecular complexes, deleterious for invaders and potentially useful for biotechnology.

PubMed: 41315870
DOI: 10.1038/s41467-025-66189-7

Experimental method

ELECTRON MICROSCOPY (3.38 Å)