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.

• 1HXW: scripts for simulation of inhibitor binding
• 1I8L CTLA-4 : B7-1

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.

1. Script for saved animation emphasizing backbone:

     #--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--

2. Script for saved animation emphasizing backbone:

     #--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--

3. Script for saved animation emphasizing contacts. Model 21 is 1HXW with the inhibitor bound, while model 1 has the inhibitor at maximum distance from the protease. The contacting residues were identified by entering the commands

   select within(4.5, (rit and model=21)) and model=21
   show residue

   The 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--

4. Script for saved animation emphasizing water contacting the inhibitor:

     #--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.

• The following views assume you have already looked at the asymmetric unit,
• Chain of 6 asymmetric unit tetramers, This type of chain is believed to form in the immunological synapse between a T lymphocyte and an antigen-presenting cell.
• 4 tetramers (asymmetric units) head to tail, showing crystal contacts,
• Chime script highlighting positions of crystal contacts.
  
• Asymmetric unit (tetramer) of 1I8L plus all crystal contacts within 25 Å [PE]. This is a pseudo-NMR file with the asymmetric unit in model 1, and the crystal contacts in model 2. In PE's QuickViews, scroll down in the upper left frame and check the box Include all models in contact surfaces. Then DISPLAY Contacts.
  
  
  
• 4 chains showing crystal contacts,
• A 3-unit cell portion of the crystal,
• More information on crystal contacts. This includes a link to the methods by which the above crystal symmetry PDB files were created with

  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.

• Here is the structure of B7-2 bound to CTLA-4,