This supplement provides details for the following molecules. It is intended that you will visit the Atlas and follow the links there for specific molecules in this Supplement.
These scripts can be pasted into the command script box on the PE's NMR Models/Animations page to produce the coloring and rendering in the four saved examples. The scripts are provided to illustrate how cases of such scripts, and so you could use them as starting points for further modifications.
#--Begin color scheme-- ## show selected false select all color red #to clear previous palette select all color cpk select protein set hetero off color group #--End color scheme-- #$ Begin animation loop #--Begin display script-- #Main display. select model=@ backbone 0.5 select model=@ and RIT wireframe 0.15 spacefill 0.45 #--End display script--
#--Begin color scheme-- ## show selected false select all color white select ligand color cpk select water color magenta #--End color scheme-- #$ Begin animation loop #--Begin display script-- select model=@ spacefill #--End display script--
select within(4.5, (rit and model=21)) and model=21 show residueThe list of contacting residues was then copied from the message window. These residues were then coded into the script so they can be highlighted in all models. Here is the script using this information:
#--Begin color scheme-- ## show selected false select all color red #to clear previous palette select all color cpk select (84,82,81,50,49,48,47,32,30,29,28,27,25,23,8) and :a select selected or ((84,82,81,80,50,49,48,47,32,30,29,28,27,25,23,8) and :b) define ritcon selected #--End color scheme-- #$ Begin animation loop #--Begin display script-- #Main display. select model=@ backbone 0.2 select model=@ and ritcon wireframe 0.35 select model=@ and RIT spacefill #--End display script--
#--Begin color scheme-- ## show selected false select all color red #to clear previous palette select all color cpk select water color magenta #contacting water select (70,51,50,41,36,1) and water define watcon selected #--End color scheme-- #$ Begin animation loop #--Begin display script-- #Main display. select model=@ backbone 0.2 select model=@ and watcon spacefill select model=@ and RIT spacefill #--End display script--
B7 is a costimulatory receptor on antigen-presenting cells, such as macrophages or dendritic cells that have taken up infectious microbes. T lymphocytes defend us against the microbes once they recognize the antigen being presented. In order for the T cells to respond effectively, they need to see B7, which they do with a cognate receptor called CD28. After the microbes have been eliminated, the T cells express another receptor known as CTLA-4. Although CTLA-4 also binds to B7, it signals the T cell to shut down, rather than to attack.
There are two forms of B7: B7-1 and B7-2. Both bind to CD28 and CTLA-4. The above structure (1I8L) is CTLA-4 bound to B7-1.