Binding of Influenza hemagglutin peptide by MHC class II and the TCR Receptor

The structure at the right shows an MHC class II alpha chain in dark blue and the MHC class II beta chain in light blue. Only the extracellular domains are shown.

Highlight the MHC II alpha chain  Backbone Space Fill Ribbons   Wife frame

Highlight the MHC II beta chain  Backbone Space Fill Ribbons Wife frame

The T cell receptor alpha chain is in green and the beta chain is in yellow-green.  Again, only extracellular domains are shown.

Highlight the TCR alpha chain Backbone Space Fill Ribbons Wife frame

Highlight the TCR beta chain  Backbone Space Fill Ribbons Wife frame

Now reset the wireframe

The MHC alpha chain also has two carbohydrate chains  Space Fill Off

Held between the four proteins, in a groove, is a peptide from the hemagglutination protein of influenza virus A. Space Fill

This can be seen better if we rotate the molecule

Let's look at the structure of the individual proteins. First convert the molecule to strands , since this shows the alpha helices and beta sheets more clearly. You can see that the two MHC II chains, alpha and beta, have one major alpha helix each and these form the walls of the cleft in which the peptide sits. We can now show the alpha helices in purple and the beta sheets in orange; random coil is in gray  .

The alpha and beta chains form hydrogen bonds with the peptide. Unlike the situation with the class I protein (in which the conserved H-bonding amino acids interact with the end of the peptide), in the class II protein hydrogen bonds are made along the length of the peptide by both the class II alpha chain and the class II beta chain    

Now rotate the molecule to show this more clearly

As in the class I MHC, there are highly variable residues. In the class II MHC moleucle these are primarily in the beta chain. The extracellular region of the beta chain can be divided into two parts, the beta-1  and the beta-2 domain . The hypervariable regions have been mapped to the beta-1 region of the molecule and line the cleft into which the peptide fits 

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The molecule can be rotated at any time by left clicking the mouse on the molecule and dragging the mouse with the left button depressed. Or you can switch on rotation using the buttons below.

To return to the original wire-frame structure, use the reload/refresh button on your browser.

Further changes and selection may be made using the Chime menu. Right click on the molecule to show the Chime menu.

© Richard Hunt, University of South Carolina School of Medicine