Protein-RNA RasMol Tutorial

Examples of Protein-RNA Co-Complexes

Just a few examples of small RNAs and their interactions with proteins

Key concepts

Recognize RNA in a widened major groove or loop region.
RNA backbone geometry can be quite unusual.

This page: directions and sample views (these can be enjoyed without running the viewer program, but you could look at a book instead).
TAR RNA - arginine PDB file, 1akx.pdb, the structure of the TAR RNA with a bound arg (mimicking the tat protein), from Williamson's group.
Rev-RRE PDB file, 1etf.pdb, from WIlliamson's group.
U1A protein-RNA interaction, 1urn.pdb, from Nagai's group.
a file of rasmol commands for display of important features of each of the three complexes.

Up to teaching resources page.

For directions on use see previous DNA tutorial.

Results

Here are gif images generated from the PDB files and scripts above.

TAR-Arg. Note Arg binding into major groove widened by the bulge.

Overview of Rev bound in the major groove of the RRE

Zoom in on GA pair in the middle of a distorted duplex, which makes room for protein to bind in the major groove.

Two views of U1A RNA RNP, showing interaction with hairpin loop residues.

Last modified 8/15/18, Jason D. Kahn

Examples of Protein-RNA Co-Complexes

Key concepts

Contents

For directions on use see previous DNA tutorial.

Results