Molecular visualization of the lambda cI repressor-DNA interaction

This web page uses the open-source Java Applet program Jmol, a proposed platform-independent replacement for Chime and Rasmol, neither of which is available in an OS X native version. You will need a relatively recent Java Virtual Machine to use it.

The buttons below are generally intended to be clicked in order.

This tutorial illustrates 1lmb.pdb, the structure of the lambda repressor by Beamer and Pabo, 1992. This shows the classic alpha helices in major groove recogntion. Note direct readout via hydrogen bonding networks in the major groove, water-mediated hydrogen bonds, indirect readout through bending and twisting of the central four base pairs, inverted repeat symmetry of the recognition site.

Protein-DNA tutorial home
Teaching resources
J. Kahn home page

Here are the text files that back up the buttons, so you can see the syntax used for Jmol. You should even be able to cut and paste from these files into the Jmol console and reproduce what the buttons do.

  1. Initial view
  2. Focus on HTH domains
  3. One half-site
  4. Spacefill protein
  5. Zoom in
  6. Details of H-bond network
  7. Re-orient