8Y7Z

Cryo-EM structure of the monomeric SPARSA gRNA-ssDNA complex

Summary for 8Y7Z

• Entry DOI: 10.2210/pdb8y7z/pdb
• EMDB information: 39027
• Descriptor: Piwi domain protein, Sir2 superfamily protein, RNA (21-mer), ... (5 entities in total)
• Functional Keywords: rna binding protein, structural protein, structural protein-rna-dna complex, structural protein/rna/dna
• Biological source: Geobacter sulfurreducens; More
• Total number of polymer chains: 4
• Total formula weight: 134355.78

Authors

Zhang, J.T.,Cui, N.,Wei, X.Y.,Jia, N. (deposition date: 2024-02-05, release date: 2024-10-16)

Primary citation

Cui, N.,Zhang, J.T.,Li, Z.,Wei, X.Y.,Wang, J.,Jia, N.
Tetramerization-dependent activation of the Sir2-associated short prokaryotic Argonaute immune system.
Nat Commun, 15:8610-8610, 2024

PubMed Abstract: Eukaryotic Argonaute proteins (eAgos) utilize short nucleic acid guides to target complementary sequences for RNA silencing, while prokaryotic Agos (pAgos) provide immunity against invading plasmids or bacteriophages. The Sir2-domain associated short pAgo (SPARSA) immune system defends against invaders by depleting NAD and triggering cell death. However, the molecular mechanism underlying SPARSA activation remains unknown. Here, we present cryo-EM structures of inactive monomeric, active tetrameric and active NAD-bound tetrameric SPARSA complexes, elucidating mechanisms underlying SPARSA assembly, guide RNA preference, target ssDNA-triggered SPARSA tetramerization, and tetrameric-dependent NADase activation. Short pAgos form heterodimers with Sir2-APAZ, favoring short guide RNA with a 5'-AU from ColE-like plasmids. RNA-guided recognition of the target ssDNA triggers SPARSA tetramerization via pAgo- and Sir2-mediated interactions. The resulting tetrameric Sir2 rearrangement aligns catalytic residue H186 for NAD hydrolysis. These insights advance our understanding of Sir2-domain associated pAgos immune systems and should facilitate the development of a short pAgo-associated biotechnological toolbox.

PubMed: 39366953
DOI: 10.1038/s41467-024-52910-5

Experimental method

ELECTRON MICROSCOPY (2.57 Å)