This page contains all the figures used in the notes on tertiary alpha helix structures. You may want to keep this page open, or print this page when going through the notes.
Please also note that this page contains pdb structure files and you need Jmol to view, and manipulate these structures.
Figure 8.1 Up-down beta strand topology in a beta barrel
Figure 8.2 Up-down beta strand barrel in Retinol Binding Protein
Beta barrel highlighted from retinol binding protein (1rbp.pdb) Use Chime to manipulate the protein and identify the structure. Try these commands:
Figure 8.3 Jelly roll topology in a beta barrel
You may find the jelly roll domain a difficult structure to pick out in a protein because it can twist and turn and appear distorted. You can, however, use this picture to help you identify the domain. The essential features are that it is like an inverted 'U' and it folds such that hydrogen bonds exist between strands 1 and 8; 2 and 7; 3 and 6; and 4 and 5. Consequently, these strands are also close to each other in the protein. Now compare this with a jelly roll domain in an actual protein in Figure 8.4
Figure 8.4 Jelly roll domain in CAP (catabolite activator protein)
The jelly roll domain was highlighted from CAP protein (1cgp.pdb) using only protein chain A and residues 18 to 98. Use appropriate Jmol commands, or scripts, to identify each strand of the jelly roll with a colour similar to the colours in Figure 8.3. That is, strand 1 (residues 18-23) = purple, strand 2 (residues 27-32) = cyan, strand 3 (residues 34-43) = magenta, strand 4 (residues 47-52) = blue, strand 5 (residues 57-65) = green, strand 6 (residues 67-70) = yellow, strand 7 (residues 78-88) = orange, strand 8 (residues 90-98) = red. You should be able to see the domain more clearly by picking out those strands that exist close to each other and are hydrogen bonded. For example, strand 1(purple) and 8 (red) should be close to each other.
Figure 8.5 Beta Sandwich Domain in beta2-microglobulin
The beta sandwich was highlighted from the B subunit of microglobulin (2hla.pdb) Use Jmol to manipulate the protein and identify the structure.
Figure 8.6 Beta helix - an example of a less frequent Beta domain in pectate lyase
The beta helix was highlighted from pectate lyase (2pec.pdb). (This was chosen as an example because I think it is a beaut structure!). Use Jmol to manipulate the protein and identify the structure. Can you see why its called a beta helix?
Figure 8.7 Orthogonal arrangement of beta strands
Beta strands in Fatty Acid Binding Protein (1ifb.pdb). Using the following commands one sheet will be highlighted in green the other in grey.