The rscb has/had a nucleic acid database which included protein dan information. Have you checked that? Eleanor
On 3 Jun 2014, at 16:51, Raji Edayathumangalam wrote: > 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 >
