This page contains all the figures used in the notes on beta sheet supersecodary structures. You may want to keep this page open, or print this page when going through the notes.
Please that this page contains pdb files and that you need Jmol to view, and manimpulate, these files.
Figure 4.0 Beta hairpin structure
Figure 4.1 Beta hairpin in Erabutoxin
This structure may also be known as a 'two-residue' beta turn because two of the four residues of the beta turn (coloured red) connecting the strands are not included as part of the strand. The other two residues of the beta turn are coloured blue and are considered part of each strand.
Extracted from coordinates of erabutoxin (a snake venom neurotoxin) residues 23 to 42 - 1qkd.pdb.
You may like to try these commands (or try others you think appropriate)
Figure 4.2 A beta meander long loops joining beta strands
See if you can identify the corner in the hairpin and manipulate the display to show the strands as a cartoon.
Extracted from coordinates of erabutoxin (a snake venom neurotoxin) residues 63 to 87 - 1qkd.pdb.
This is a very stylised 'topology' (see also Figures 4.8 and 4.9 below) diagram of the Greek Key motif. The light blue arrows of the motif represent beta strands and the green lines are the connecting loops. The motif is overlaid on the Greek Key pattern seen on Greek Urns. The Greek Key motif has different aspects to it and these are labelled A to D. The essential features of this structure are that there are four sequentially connected adjacent beta strands and the N-terminal strand and C-terminal strand are adjacent to each other.
Figure 4.5 Greek Key Motif in gamma crystallin
The adjacent beta strands (strands 1 through 4 - from N-terminal to C-terminal) making up the greek key motif are coloured blue, cyan, green, and yellow respectively. The strands are not perfectly aligned, and strand 3 (coloured green) is not in the same plane as the other three strands, but the essential features are apparent. That is: four sequentially connected antiparallel strands with the first and last strands next to each other.
The motif was extracted from the coordinates of gamma crystallin (1amm.pdb) restricted to one domain (residues 1-81) and then using residues 41 to 81 to visualise the motif.
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Figure 4.6 Greek Key Motif as it occurs in Staphylococcus Nuclease
The Greek Key motif in this protein may be difficult to see because of the 'break' in the first strand of the motif (residues 6 to 10 and then 13 to 19) and the fact that the strands are not as geometically aligned, or even in the same plane, as suggested in Figure 4.4.
The motif was extracted from the coordinates of Stapylococcus nuclease 1stn.pdb
You may like to try these commands (or others you may think appropriate):
Figure 4.7 Greek Key Motif - modified from Staphylococcus Nuclease
In this visualisation the two pieces of the first strand of the greek key motif shown in Figure 4.6 have been 'joined' and it is now easier to see how the first strand is 'adjacent' to the last strand. You should also observe the long connecting loop and the helix between the third and the fourth strand in the motif.
Here is the nuclease file You may like to try these commands (or others you may think appropriate):
Figure 4.8 Topology of supersecondary structures in gamma crystallin using TOPS
See if you can manipulate the structure of gamma crystallin in Figure 4.6 to match the topology diagram below (you will have to select all atoms and display the cartoon feature and you may need to open another window in your browser to help you compare)
Figure 4.9 Topology of supersecondary structures in Staphylococcus Nuclease using TOPS
As for figure 4.8 see if you can match the protein secondary structure with the diagram below (do you notice any inconsistancy?)
