3HXM: Structure Of An Argonaute Complexed With Guide Dna And Target Rna Duplex Containing Two Mismatches

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.
PDB ID: 3HXMDownload
MMDB ID: 77192
PDB Deposition Date: 2009/6/21
Updated in MMDB: 2009/10
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Source Organism:
Thermus thermophilus HB27
Similar Structures:
Biological Unit for 3HXM: trimeric; determined by author and by software (PISA)
Molecular Components in 3HXM
Label Count Molecule
Protein (1 molecule)
Molecule annotation
Nucleotides(2 molecules)
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')
Molecule annotation
RNA (5'- R(*up*ap*up*ap*cp*ap*ap*cp*up*cp*ap*cp*up*ap*cp*cp*up*cp*gp*u)-3')
Molecule annotation
Chemical (1 molecule)
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Citing MMDB