Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Activation mechanism of a short argonaute-TIR prokaryotic immune system.
Journal, issue, pages	Sci Adv, Vol. 9, Issue 29, Page eadh9002, Year 2023
Publish date	Jul 21, 2023
Authors	Dongchun Ni / Xuhang Lu / Henning Stahlberg / Babatunde Ekundayo /
PubMed Abstract	Short prokaryotic argonaute (pAgo) and toll/interleukin-1 receptor/resistance protein (TIR)-analog of PAZ (APAZ) form a heterodimeric SPARTA complex that provides immunity to its prokaryotic host ...Short prokaryotic argonaute (pAgo) and toll/interleukin-1 receptor/resistance protein (TIR)-analog of PAZ (APAZ) form a heterodimeric SPARTA complex that provides immunity to its prokaryotic host through an abortive infection mechanism. Monomeric SPARTA senses foreign RNA/DNA duplexes to assemble an active tetramer resulting in cell death by nicotinamide adenine dinucleotide (oxidized form) (NAD) depletion via an unknown mechanism. We report nine structures of SPARTA in different functional states at a resolution range of 4.2 to 2.9 angstroms, revealing its activation mechanism. Inactive SPARTA monomers bind to RNA/DNA duplexes to form symmetric dimers mediated by the association of Ago subunits. The initiation of tetramer assembly induces flexibility of the TIR domains enabling a symmetry-breaking rotational movement of a TIR domain in the dimer units which facilitates the TIR oligomerization, resulting in the formation of the substrate binding pocket and the activation of the SPARTA complex's NADase activity. Our findings provide detailed structural and mechanistic insights into activating a short argonaute defense system.
External links	Sci Adv / PubMed:37467330 / PubMed Central
Methods	EM (single particle)
Resolution	2.91 - 4.85 Å
Structure data	17299 8oz6 EMDB-17299, PDB-8oz6: cryoEM structure of SPARTA complex ligand-free Method: EM (single particle) / Resolution: 3.97 Å EMDB-17300: Duplex-bound tetramer high-resolution (EMDB-xxxx) SPARTA complex Method: EM (single particle) / Resolution: 3.1 Å EMDB-17301: Dimer-1 SPARTA complex Method: EM (single particle) / Resolution: 3.31 Å EMDB-17302: Dimer-2 SPARTA complex Method: EM (single particle) / Resolution: 3.8 Å EMDB-17303: monomer-duplex bound Method: EM (single particle) / Resolution: 4.85 Å 17304 8ozc EMDB-17304, PDB-8ozc: cryoEM structure of SPARTA complex heterodimer apo Method: EM (single particle) / Resolution: 4.0 Å 17305 8ozd EMDB-17305, PDB-8ozd: cryoEM structure of SPARTA complex dimer-3 Method: EM (single particle) / Resolution: 3.89 Å 17306 8oze EMDB-17306, PDB-8oze: cryoEM structure of SPARTA complex dimer high resolution Method: EM (single particle) / Resolution: 2.91 Å 17307 8ozf EMDB-17307, PDB-8ozf: cryoEM structure of SPARTA complex Tetramer Post-NAD cleavage-2 Method: EM (single particle) / Resolution: 3.73 Å 17308 8ozg EMDB-17308, PDB-8ozg: cryoEM structure of SPARTA complex Tetramer Post-NAD cleavage-1 Method: EM (single particle) / Resolution: 3.37 Å 17310 8ozi EMDB-17310, PDB-8ozi: cryoEM structure of SPARTA complex pre-NAD cleavage Method: EM (single particle) / Resolution: 3.22 Å
Chemicals	ChemComp-AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL ChemComp-MG: Unknown entry ChemComp-NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide
Source	maribacter polysiphoniae (bacteria)
Keywords	ANTIVIRAL PROTEIN / SPARTA / TIR / prokaryotic argonaute / DNA BINDING PROTEIN / IMMUNE SYSTEM