3DLH

Crystal structure of the guide-strand-containing Argonaute protein silencing complex

Summary for 3DLH

• Entry DOI: 10.2210/pdb3dlh/pdb
• Related: 3DLB
• Descriptor: Argonaute, DNA (5'-D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*DAP*DTP*DAP*DGP*DT)-3'), MAGNESIUM ION, ... (7 entities in total)
• Functional Keywords: argonaute, protein-dna complex, plasmid, nucleic acid binding protein-dna complex, nucleic acid binding protein/dna
• Biological source: Thermus thermophilus
• Total number of polymer chains: 4
• Total formula weight: 167167.13

Authors

Wang, Y.,Sheng, G.,Patel, D.J. (deposition date: 2008-06-27, release date: 2008-09-02, Last modification date: 2024-02-21)

Primary citation

Wang, Y.,Sheng, G.,Juranek, S.,Tuschl, T.,Patel, D.J.
Structure of the guide-strand-containing argonaute silencing complex.
Nature, 456:209-213, 2008

PubMed Abstract: The slicer activity of the RNA-induced silencing complex is associated with argonaute, the RNase H-like PIWI domain of which catalyses guide-strand-mediated sequence-specific cleavage of target messenger RNA. Here we report on the crystal structure of Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-base DNA guide strand, thereby identifying the nucleic-acid-binding channel positioned between the PAZ- and PIWI-containing lobes, as well as the pivot-like conformational changes associated with complex formation. The bound guide strand is anchored at both of its ends, with the solvent-exposed Watson-Crick edges of stacked bases 2 to 6 positioned for nucleation with the mRNA target, whereas two critically positioned arginines lock bases 10 and 11 at the cleavage site into an unanticipated orthogonal alignment. Biochemical studies indicate that key amino acid residues at the active site and those lining the 5'-phosphate-binding pocket made up of the Mid domain are critical for cleavage activity, whereas alterations of residues lining the 2-nucleotide 3'-end-binding pocket made up of the PAZ domain show little effect.

PubMed: 18754009
DOI: 10.1038/nature07315

Experimental method

X-RAY DIFFRACTION (3 Å)