8QLP

CryoEM structure of the RNA/DNA bound SPARTA (BabAgo/TIR-APAZ) tetrameric complex

Summary for 8QLP

• Entry DOI: 10.2210/pdb8qlp/pdb
• EMDB information: 18487
• Descriptor: Toll/interleukin-1 receptor domain-containing protein, Short prokaryotic Argonaute, RNA (5'-R(*AP*UP*GP*AP*CP*GP*GP*CP*UP*CP*UP*AP*AP*UP*CP*UP*AP*UP*UP*AP*GP*U)-3'), ... (5 entities in total)
• Functional Keywords: prokaryotic argonaute, tir domain, rna binding protein, dna binding protein, immune system, oligomerization, nadase activity
• Biological source: Bacillales bacterium; More
• Total number of polymer chains: 16
• Total formula weight: 501259.23

Authors

Finocchio, G.,Koopal, B.,Potocnik, A.,Heijstek, C.,Jinek, M.,Swarts, D. (deposition date: 2023-09-20, release date: 2024-01-31, Last modification date: 2024-03-06)

Primary citation

Finocchio, G.,Koopal, B.,Potocnik, A.,Heijstek, C.,Westphal, A.H.,Jinek, M.,Swarts, D.C.
Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA.
Nucleic Acids Res., 52:2012-2029, 2024

PubMed Abstract: In both prokaryotic and eukaryotic innate immune systems, TIR domains function as NADases that degrade the key metabolite NAD+ or generate signaling molecules. Catalytic activation of TIR domains requires oligomerization, but how this is achieved varies in distinct immune systems. In the Short prokaryotic Argonaute (pAgo)/TIR-APAZ (SPARTA) immune system, TIR NADase activity is triggered upon guide RNA-mediated recognition of invading DNA by an unknown mechanism. Here, we describe cryo-EM structures of SPARTA in the inactive monomeric and target DNA-activated tetrameric states. The monomeric SPARTA structure reveals that in the absence of target DNA, a C-terminal tail of TIR-APAZ occupies the nucleic acid binding cleft formed by the pAgo and TIR-APAZ subunits, inhibiting SPARTA activation. In the active tetrameric SPARTA complex, guide RNA-mediated target DNA binding displaces the C-terminal tail and induces conformational changes in pAgo that facilitate SPARTA-SPARTA dimerization. Concurrent release and rotation of one TIR domain allow it to form a composite NADase catalytic site with the other TIR domain within the dimer, and generate a self-complementary interface that mediates cooperative tetramerization. Combined, this study provides critical insights into the structural architecture of SPARTA and the molecular mechanism underlying target DNA-dependent oligomerization and catalytic activation.

PubMed: 38224450
DOI: 10.1093/nar/gkad1248

Experimental method

ELECTRON MICROSCOPY (3.14 Å)