Interactive Protein Tutorial

Sequence and structure of SH3 domains

We will examine structure and function of an SH3 (src homology 3) domain by exploring the interaction of the Fyn SH3 domain (PDB = 1AZG) with a peptide ligand. Remember Fyn is a member of the Src family of non-receptor tyrosine kinases and the general lessons that you will learn here can be applied to the SH3 domains of other members of this family as well as the same domain in other protein families. You may care to remember this when studying pp60c-Src kinase at other points in CELL2007 and CELL2008 part 2. You should also contrast this information with that on SH3 domains is Branden and Tooze.

The peptide ligand

We will begin our study of Fyn-SH3 domain structure and function by examining an example of the peptide ligands that it is known to bind. Here is a short segment of this sort of a ligand. Stop this peptide from spinning and orient it so that you can look directly along the length of this backbone with the yellow N-terminus towards you and the blue C-terminus away from you and going into the screen. You will notice that the molecule appears to be triangular in cross section, think of a triangular prism like a toblerone box. In other words there are three residues per turn. Since this is turning anti-clockwise this is a right-handed helix.

Ligand proline residues

To be exact, this is a Type II polyproline helix, the proline residues are shown in red.

Ligand side chains

The backbone α-carbon representation does not give a good impression of the overall structure. You can get a better idea with the side chains added.

Non-SH3 domain-binding residues

You should also remember that this is the SH3 domain binding region of the peptide ligand and that it is only part of the larger molecule. Some more residues are shown here. You should still be able to make out the triangular cross-section.

Interaction with the SH3 domain

We can add representations of the structure of the SH3 domain. Here is a ball and stick model, notice that the region of the peptide ligand that spans this compact domain is the polyproline region.

Individual amino acids on the surface of the SH3 domain

Here we can see a spacefilled version of the SH3 domain. You should be able to make out the side chains of some amino acids that lie near the peptide ligand.

Note: If you re-start this tutorial and reach this point again you may like to view the surface of the SH3 domain to see how tightly the ligand fits into the grooves on the surface. You can do this by using you right hand mouse button now. Try to remove the space fill form and then create a "Molecular Surface", be patient. Use the right hand button to select the protein components, change the view to strands (style > structures > strands) then create a molecular surface (surfaces > molecular surface).

Secondary structure in SH3 domains

Here you can see that there are only a handfull of secondary structural elements in an SH3 domain. The main feature is a twisted beta sheet that is so deformed that it forms two smaller orthogonal sheets. In this particular domain there is also a short region with α-helical geometry, although this is not typical of these domains. The other major and notable features are the loops connecting the β sheets.

Loops

Two loops in particuar should be noted: The RT-loop (beta 1 to beta 2) and the n-Src loop (beta 3 to beta 4). Make sure that you can identify these beta strands and these loops by using secondary structural details. Remember that this is chain B in this solution to the structure, E= a beta strand residue and the loops lie between clusters of consequtive E's. For orientation the N-terminal residue can be coloured blue and the C-terminal residue yellow with this button.

Planar side chains locate the ligand helix

The packing of the type II polyproline helix against the SH3 domain is rather like pushing the ends of two screws together so that the helical threads overlap. The "thread" on the SH3 domain is formed from the planar side chains of the aromatic amino acids tyrosine and tryptophan. The key residues here are Y91, Y137 and W119 and they all lie along a ridge parallel to the length of the peptide ligand.

The role of proline residues in the ligand

Here we can see more clearly how the side chains of the ligand pack between these hydrophobic residues on the surface of the SH3 domain. Note the key role of the proline rings (red) in addition to enforcing the geometry necessary for a stable type II helix (remember the Ramachandran plot?). Image source Wikipedia.

A screw thread

Here is a spacefill view to reinforce the "screwthread" point of view.

A screwthread, part 2

The same point made with dots for clarity.

Ridges and grooves

Here we can see that the surface of the correctly "wound" peptide and an SH3 domain are complementary.

Planar side chains locate the ligand helix

We can still see that the planes of the SH3 aromatic residues responsible for packing against the peptide are prominent on the domain surface.

Final representation

The point can be reinforced by including the backbone of the ligand. The N-terminus is coloured blue and the C-terminus orange.
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