3HXM

Structure of an argonaute complexed with guide DNA and target RNA duplex containing two mismatches.

Summary for 3HXM

• Entry DOI: 10.2210/pdb3hxm/pdb
• Related: 3DLB 3DLH 3F73 3HGE 3HJF 3HK2
• Descriptor: Argonaute, DNA (5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3'), RNA (5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3'), ... (4 entities in total)
• Functional Keywords: argonaute, protein-dna-rna complex, nucleic acid binding protein-dna-rna complex, nucleic acid binding protein/dna/rna
• Biological source: Thermus thermophilus
• Total number of polymer chains: 3
• Total formula weight: 89590.05

Authors

Wang, Y.,Li, H.,Sheng, G.,Patel, D.J. (deposition date: 2009-06-21, release date: 2009-10-06, Last modification date: 2023-09-06)

Primary citation

Wang, Y.,Juranek, S.,Li, H.,Sheng, G.,Wardle, G.S.,Tuschl, T.,Patel, D.J.
Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes.
Nature, 461:754-761, 2009

PubMed Abstract: The slicer activity of the RNA-induced silencing complex resides within its Argonaute (Ago) component, in which the PIWI domain provides the catalytic residues governing guide-strand mediated site-specific cleavage of target RNA. Here we report on structures of ternary complexes of Thermus thermophilus Ago catalytic mutants with 5'-phosphorylated 21-nucleotide guide DNA and complementary target RNAs of 12, 15 and 19 nucleotides in length, which define the molecular basis for Mg(2+)-facilitated site-specific cleavage of the target. We observe pivot-like domain movements within the Ago scaffold on proceeding from nucleation to propagation steps of guide-target duplex formation, with duplex zippering beyond one turn of the helix requiring the release of the 3'-end of the guide from the PAZ pocket. Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures.

PubMed: 19812667
DOI: 10.1038/nature08434

Experimental method

X-RAY DIFFRACTION (3.1 Å)