Symmetry
issues in PDB filesSymmetry
issues in PDB files
A PDB file contains the minimum amount of information necessary to describe completely the crystal structure of the molecule or molecules. In some cases, including those dealing with protein-DNA interactions, this information may not be sufficient to display the biologically relevant structure.
Consider a protein-DNA interaction involving a completely symmetrical DNA sequence bound by a protein dimer. If the two subunits of the dimer are also completely symmetrical (a form of symmetry called 2-fold rotational symmetry), then it is possible that the complex will crystallize with only a portion of the biologically relevant molecule in the crystal's asymmetric unit, which is the unique portion of the crystal. In these cases, a symmetry element such as a two-fold rotation axis will run completely through the crystal and also through the molecule, so that a complete molecule consists of two asymmetric units related by two-fold rotation symmetry. The PDB file will only contain the one asymmetric unit, however. Clearly, you would be interested in having both DNA strands and both protein subunits. Here is how to get that information, given with an example that illustrates the concern.
When you link to the RCSB, you get a home page that invites you to enter a PDB accession number, if you know it, in a box on the right under "Search". Enter "2DGC" and click on Explore. This gives you the page for this structure (GCN4 bound to DNA). Notice that in the thumbnail view of the structure at the upper right there is only one alpha helix visible. This is a tip-off that you have the symmetry problem, since you expect to find two helices. Note that it's really helpful to know something about your protein, if you want to be sure to avoid this concern. All the PDB files that I've put on the server are complete.
A description describing this issue, from the RCSB, is here. It also describes a computational method for generating the biological molecule. A simpler way is the following. On the main page for a given structure, there's a menu at the top right "Download Files". Clicking on this gives a list, and one of the options is "Biological Unit". Click on that and you will download the proper structure instead of the asymmetric unit.
If you try this for other proteins, let me know if it works!
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