9JHM

Cryo-EM structure of CpAgo_gDNA-tg_bubble_dsDNA monomeric ternary complex

Summary for 9JHM

• Entry DOI: 10.2210/pdb9jhm/pdb
• EMDB information: 61487
• Descriptor: Clostridium perfringen Argonaute, DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), DNA (58-MER), ... (4 entities in total)
• Functional Keywords: pagos, nucleotide-binding pocket, paz, cryo-em, dna binding protein/dna, dna binding protein-dna complex
• Biological source: Clostridium perfringens; More
• Total number of polymer chains: 3
• Total formula weight: 110649.96

Authors

Liu, Y.,Li, S.,Zhang, K. (deposition date: 2024-09-10, release date: 2025-07-30, Last modification date: 2026-02-18)

Primary citation

Liu, Y.,Zhang, J.,Liu, J.,Zhang, S.,An, L.,Xie, W.,Zhang, K.,Li, S.
The PAZ pocket and dimerization drive CpAgo's guide-independent and DNA-guided dual catalysis.
Nat Commun, 16:6599-6599, 2025

PubMed Abstract: Argonaute proteins (Agos) play essential roles in nucleic acid targeting across life domains. While eukaryotic Agos (eAgos) utilize small-interfering RNAs (siRNAs) or microRNAs (miRNAs) for RNA interference, the mechanisms driving prokaryotic Agos (pAgos) in bacterial defense remain underexplored. Here, we characterize the mesophilic pAgo from Clostridium perfringens (CpAgo), which exhibits robust guide-independent and DNA-guided activity at 37 °C. CpAgo efficiently degrades plasmids and structured RNAs into small fragments, generating DNA fragments that serve as guides for subsequent cleavage. Cryo-electron microscopy reveals a positively-charged PAZ nucleotide-binding pocket, critical for both guide-dependent and guide-independent substrate recognition and cleavage. Structural analysis identifies CpAgo's dimerization as a prerequisite for catalytic activity, supporting both nucleic acid degradation and targeted action. Functional assays in Escherichia coli demonstrate CpAgo's role in bacterial defense by mediating plasmid degradation and DNA-guided cleavage. These findings position CpAgo as a critical component of prokaryotic immunity and a promising tool for biotechnology.

PubMed: 40675991
DOI: 10.1038/s41467-025-61926-4

Experimental method

ELECTRON MICROSCOPY (3.2 Å)