8QLP image
Entry Detail
PDB ID:
8QLP
EMDB ID:
Keywords:
Title:
CryoEM structure of the RNA/DNA bound SPARTA (BabAgo/TIR-APAZ) tetrameric complex
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-09-20
Release Date:
2024-01-31
Method Details:
Experimental Method:
Resolution:
3.14 Å
Aggregation State:
HELICAL ARRAY
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Toll/interleukin-1 receptor domain-containing protein
Chain IDs:A, E, I, M
Chain Length:452
Number of Molecules:4
Biological Source:Bacillales bacterium
Polymer Type:polypeptide(L)
Description:Short prokaryotic Argonaute
Chain IDs:B, F, J, N
Chain Length:507
Number of Molecules:4
Biological Source:Bacillales bacterium
Polymer Type:polyribonucleotide
Description: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')
Chain IDs:C, G, K, O
Chain Length:21
Number of Molecules:4
Biological Source:Bacillales bacterium
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*CP*TP*AP*AP*TP*AP*GP*AP*TP*TP*AP*GP*AP*GP*CP*CP*GP*TP*C)-3')
Chain IDs:D, H, L, P
Chain Length:25
Number of Molecules:4
Biological Source:Bacillales bacterium
Ligand Molecules
Primary Citation
Target DNA-dependent activation mechanism of the prokaryotic immune system SPARTA.
Nucleic Acids Res. 52 2012 2029 (2024)
PMID: 38224450 DOI: 10.1093/nar/gkad1248

Abstact

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.

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Primary Citation of related structures