SNAP output for PDB entry 3hxm [SNAP web server]

PDB-id

3hxm; SNAP-derived features in text and JSON formats; DNAproDB

Class

nucleic acid binding protein-DNA-RNA

Method

X-ray (3.1 Å)

Summary

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

Reference

Wang Y, Juranek S, Li H, Sheng G, Wardle GS, Tuschl T, Patel DJ (2009): "Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes." Nature, 461, 754-761. doi: 10.1038/nature08434.

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.