Protein Name

RNase III (D44N) complexed with double-stranded RNA


Aquifex aeolicus (bacteria,thermophile)

Biological Context

RNA interference is one of the most surprising discoveries in the last ten years. The RNA interference system checks the existence of double-stranded RNAs (dsRNA) in cells and when dsRNAs are detected, the system destroys them. RNA interference system exists in all organisms, from as simple as bacteria to as complex as humans. One of the reasons why this system has been evolutionarily conserved is its usefulness as a defence against certain types of viruses. Viruses produce dsRNA during their reproductive cycle and at that time they can be efficiently eliminated by the RNA interference system. Now, RNA interference, originally used by living organisms to protect them from viruses, became a useful technique to stop a specific gene expression in basic science laboratories. In the near future it is expected that it be applied to the clinical fields. The RNA interference technique is composed of five steps.

1) Introduction of a dsRNA that has complementary sequence with a target gene the function of which is to be interfered. 2) Detection of the dsRNA by a protein complex containing an RNA nuclease, RNase (enzyme that degrades RNA), and an RNA helicase. 3) Destruction of the dsRNAs. Long RNAs are cut into short RNAs (of approximately 23 base pairs), which remain bound with the protein complex. 4) Recognition of the RNAs transcribed from the target gene by the complementary RNA fragments in the protein complex. 5) Destruction of the RNAs of the target gene by the RNase in the protein complex, resulting in gene-silencing.

The detailed mechanism of recognition of dsRNA by RNase in the protein complex was unclear.

Structure Description


The structure shown here shed a light on this issue. This is the complex structure of an RNase called RNase III and dsRNA, corresponding to the step 3 above. RNase III is specific to dsRNA (and not to single-stranded RNA). It has the RNase III signature motif in its active center and produces two-base 3’ overhanging RNA pieces. The substrate dsRNA is recognized by the four RNA binding motifs in RNase III with three protein-interacting boxes in dsRNA. The 7-residue liker of the RNase III helps induced fit in protein-RNA recognition. Scissile-bond cleavage of dsRNA is catalyzed by conserved amino acid residues and divalent cations.

Protein Data Bank (PDB)



  • Gan, J. Tropea, J.E. Austin, B.P. Court, D.L. Waugh, D.S. Ji, X.; "Structural Insight into the Mechanism of Double-Stranded RNA Processing by Ribonuclease III."; Cell (Cambridge,Mass.); (2006) 124:355-366 PubMed:16439209.


author: Sachiyo Nomura

Japanese version:PDB:2EZ6