4F1N

Crystal structure of Kluyveromyces polysporus Argonaute with a guide RNA

Summary for 4F1N

• Entry DOI: 10.2210/pdb4f1n/pdb
• Descriptor: KpAGO, RNA 5'-R(P*UP*AP*AP*AP*AP*AP*AP*AP*A)-3' (3 entities in total)
• Functional Keywords: argonaute, rnai, rnase h, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Vanderwaltozyma polyspora; More
• Total number of polymer chains: 4
• Total formula weight: 241390.63

Authors

Nakanishi, K.,Weinberg, D.E.,Bartel, D.P.,Patel, D.J. (deposition date: 2012-05-07, release date: 2012-06-13, Last modification date: 2024-02-28)

Primary citation

Nakanishi, K.,Weinberg, D.E.,Bartel, D.P.,Patel, D.J.
Structure of yeast Argonaute with guide RNA.
Nature, 486:368-374, 2012

PubMed Abstract: The RNA-induced silencing complex, comprising Argonaute and guide RNA, mediates RNA interference. Here we report the 3.2 Å crystal structure of Kluyveromyces polysporus Argonaute (KpAGO) fortuitously complexed with guide RNA originating from small-RNA duplexes autonomously loaded by recombinant KpAGO. Despite their diverse sequences, guide-RNA nucleotides 1-8 are positioned similarly, with sequence-independent contacts to bases, phosphates and 2'-hydroxyl groups pre-organizing the backbone of nucleotides 2-8 in a near-A-form conformation. Compared with prokaryotic Argonautes, KpAGO has numerous surface-exposed insertion segments, with a cluster of conserved insertions repositioning the N domain to enable full propagation of guide-target pairing. Compared with Argonautes in inactive conformations, KpAGO has a hydrogen-bond network that stabilizes an expanded and repositioned loop, which inserts an invariant glutamate into the catalytic pocket. Mutation analyses and analogies to ribonuclease H indicate that insertion of this glutamate finger completes a universally conserved catalytic tetrad, thereby activating Argonaute for RNA cleavage.

PubMed: 22722195
DOI: 10.1038/nature11211

Experimental method

X-RAY DIFFRACTION (3.187 Å)