Virtuelle (Nano) Welten PDB Molecule of the Month 98: Small Interfering RNA (siRNA)

Exploring the Structure

The siRNA molecules made by dicer are easy to recognize: they are a uniform length, and they have an unusual overhang of bases at each end. The structure shown in blue here, from PDB entry 1si3, is the "PAZ" domain used by many proteins to recognize the ends of siRNA (a small piece of an siRNA is shown in orange). Notice how the overhanging bases bind into a small pocket, and the exposed base at the end of the shorter strand is covered by a little shelf of protein.

These pictures were created with RasMol. To create similar pictures, you can click on the accession codes here and pick one of the options under Images and Visualization. To see the scientific papers used to research this Molecule of the Month, click here. Also available are related entries in the PDB as determined by a keyword search on January 30, 2008 for siRNA OR "RNA interference".