Hi Sophie, The crystal structure of winged helix protein/transcription factor HNF-3gamma bound to DNA comes to mind. Also, other transcription factors of that ilk would be worth looking at.
Also, if you are looking for proteins that bend DNA in a sequence-independent manner, one of the best examples to my knowledge is the crystal structure of the nucleosome core particle (PDB id, 1aoi). With histones having the job of compressing all of our genomic DNA into discs-like nucleosome core particles (NCP), you may find it very informative to see the many specifics of how histones bind the 146-bp DNA in a sequence-independent fashion and bend the 146-bp DNA every or so base pairs throughout the length of 146 base pairs. Look up Luger et al., 1997 (Nature) and related publications where the sequence-independent bending of DNA is discussed in great detail. Hope this helps. Raji On Tue, Jun 3, 2014 at 9:25 AM, Sophie Bliss <mbp1...@sheffield.ac.uk> wrote: > Hello, > > I was wondering if anyone knows of a method that can be used to search > the PDB for DNA/RNA structures (essentially a Dali search for > DNA/RNA)? > > I have recently obtained a 2.3 A protein structure bound in complex > with DNA. X3DNA has shown the DNA to be B-form generally but the 3DNA > output and the structure both show a significant bend in the DNA > chain. Other than apparently non-specific nuclease activity, we do > not know the function of the protein in vivo. It would be very useful > to be able to look at other proteins that bind DNA/RNA that > target/produce similar bends in DNA/RNA structure, independent of base > sequence. However, with thousands of structures in the PDB containing > DNA it would be impossible to do this by eye! Thanks for reading, I > look forward to hearing your suggestions. > > Sophie, > Sheffield University > -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University
