8U72 image
Entry Detail
PDB ID:
8U72
EMDB ID:
EMD-41966
Keywords:
RNA BINDING PROTEIN/RNA/DNA
Title:
Cryo-EM structure of the SPARTA oligomer with guide RNA and target DNA
Biological Source:
Source Organism:
Thermoflavifilum thermophilum, synthetic construct
Host Organism:
Escherichia coli
PDB Version:
Deposition Date:
2023-09-14
Release Date:
2024-06-12
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.15 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
8U72 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:TIR domain-containing protein
Chain IDs:C (auth: H), L (auth: D), M (auth: B), O (auth: F)
Chain Length:450
Number of Molecules:4
Biological Source:Thermoflavifilum thermophilum
UniProt ID:A0A1I7NFG5 Pfam ID:PF13676
Protein Blast
Polymer Type:polypeptide(L)
Description:Piwi domain-containing protein
Chain IDs:D (auth: I), E, N (auth: C), P (auth: G)
Chain Length:507
Number of Molecules:4
Biological Source:Thermoflavifilum thermophilum
UniProt ID:A0A1I7NFD7
Polymer Type:polyribonucleotide
Description:RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*A)-3')
Chain IDs:A (auth: U), F (auth: M), H (auth: S), J (auth: X)
Chain Length:21
Number of Molecules:4
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*TP*AP*TP*AP*CP*AP*AP*CP*CP*TP*AP*CP*TP*AP*CP*CP*TP*C)-3')
Chain IDs:B (auth: V), G (auth: N), I (auth: T), K (auth: Y)
Chain Length:45
Number of Molecules:4
Biological Source:synthetic construct
Ligand Molecules
MG
Primary Citation
Nucleic acid mediated activation of a short prokaryotic Argonaute immune system.
Nat Commun 15 4852 4852 (2024)
PMID: 38844755 DOI: 10.1038/s41467-024-49271-4

Abstact

A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P)+ hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15-3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.

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Disease

Primary Citation of related structures
8U72