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 of the SPARDA defense system by filament assembly using a beta-relay signaling mechanism widespread in prokaryotic Argonautes.
Journal, issue, pages	Cell Res, Vol. 35, Issue 12, Page 1056-1078, Year 2025
Publish date	Nov 27, 2025
Authors	Edvinas Jurgelaitis / Evelina Zagorskaitė / Aurimas Kopūstas / Simonas Asmontas / Elena Manakova / Indrė Dalgėdienė / Ugnė Tylenytė / Arunas Silanskas / Paulius Toliusis / Algirdas Grybauskas / Marijonas Tutkus / Česlovas Venclovas / Mindaugas Zaremba
PubMed Abstract	Present in all three domains of life, Argonaute proteins use short oligonucleotides as guides to recognize complementary nucleic acid targets. In eukaryotes, Argonautes are involved in RNA silencing, ...Present in all three domains of life, Argonaute proteins use short oligonucleotides as guides to recognize complementary nucleic acid targets. In eukaryotes, Argonautes are involved in RNA silencing, whereas in prokaryotes, they function in host defense against invading DNA. Here, we show that SPARDA (short prokaryotic Argonaute, DNase associated) systems from Xanthobacter autotrophicus (Xau) and Enhydrobacter aerosaccus (Eae) function in anti-plasmid defense. Upon activation, SPARDA nonspecifically degrades both invader and genomic DNA, causing host death, thereby preventing further spread of the invader in the population. X-ray structures of the apo Xau and EaeSPARDA complexes show that they are dimers, unlike other apo short pAgo systems, which are monomers. We show that dimerization in the apo state is essential for inhibition of XauSPARDA activity. We demonstrate by cryo-EM that activated XauSPARDA forms a filament. Upon activation, the recognition signal of the bound guide/target duplex is relayed to other functional XauSPARDA sites through a structural region that we termed the "beta-relay". Owing to dramatic conformational changes associated with guide/target binding, XauSPARDA undergoes a "dimer-monomer-filament" transition as the apo dimer dissociates into the guide/target-loaded monomers that subsequently assemble into the filament. Within the activated filament, the DREN nuclease domains form tetramers that are poised to cleave dsDNA. We show that other SPARDAs also form filaments during activation. Furthermore, we identify the presence of the beta-relay in pAgo from all clades, providing new insights into the structural mechanisms of pAgo proteins. Taken together, these findings reveal the detailed structural mechanism of SPARDA and highlight the importance of the beta-relay mechanism in signal transduction in Argonautes.
External links	Cell Res / PubMed:41298897 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	1.5 - 3.0 Å
Structure data	53008 9qcc EMDB-53008, PDB-9qcc: Activated XauSPARDA filament assembly with bound dsDNA substrate Method: EM (single particle) / Resolution: 3.0 Å PDB-9qbl: Crystal structure of Xanthobacter autotrophicus SPARDA mutant lacking DREN nuclease domains Method: X-RAY DIFFRACTION / Resolution: 1.5 Å PDB-9qbp: Crystal structure of Enhydrobacter aerosaccus apo SPARDA complex Method: X-RAY DIFFRACTION / Resolution: 2.45 Å PDB-9qbq: Crystal structure of apo SPARDA complex from Xanthobacter autotrophicus Method: X-RAY DIFFRACTION / Resolution: 3 Å
Chemicals	ChemComp-ACY: ACETIC ACID ChemComp-GOL: GLYCEROL ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / pH bufferYM ChemComp-PEG: DI(HYDROXYETHYL)ETHER ChemComp-CL: Unknown entry ChemComp-BME: BETA-MERCAPTOETHANOL ChemComp-TAR: D(-)-TARTARIC ACID ChemComp-HOH: WATER ChemComp-SO4: SULFATE ION ChemComp-CA*: Unknown entry
Source	xanthobacter autotrophicus py2 (bacteria) escherichia coli (E. coli) enhydrobacter aerosaccus (bacteria)
Keywords	RNA BINDING PROTEIN / Protein-nucleic acid interactions / Argonaute / pAgo / guide and target specificity / short prokaryotic Argonaute / bacterial defence system / DREN domain / DREN-APAZ