Here is a jmol representation of an MHC class I molecule. Use the buttons below to explore the parts of MHC class I. Also, you can hold shift and click to easily zoom in and out, and you can hold shift and double-click to move the molecule around the black interface.
Click here to reset MHC class I.
Here's a view of the backbone of the molecule. The small bright green segment is the particular peptide bound by this MHC class I molecule. The large light blue polypeptide represents the three α subunits, while the light green polypeptide represents the β2 microglobulin subunit.
This differentiates between the β pleated sheets and α helices in the structure. Notice that the pair of parallel pink α helices form the peptide binding groove. One of the helices belongs to the α1 domain and the other to the α2 domain. In MHC class I, molecular interactions cause this groove to be "closed" on both ends (as opposed to an MHC class II molecule, which is "open" on both ends).1 β pleated sheets form the base of the groove. The blinking peptide is anchored within the groove formed by these α helices and β sheets, and T cell receptors can bind here and determine the pathogenicity of this antigen.
Now let's examine the β2 microglobulin subunit in more detail. It consists of two large β sheets which appear in the interface as the Van der Waals forces fade and the ribbon enlarges. One β structure consists of four strands, and the other has three. These two β sheets are linked by a disulfide bond (represented by the blinking lines). The blue end is the amino terminus, while the yellow end is the carboxy terminus. This subunit is so highly conserved that one species may use the β2 microglobulin from another species and retain functional MHC class I molecules. 2
In addition to the β2 microglobulin subunit, MHC class I is composed of three α subunits. This animation distinguishes between the α1, α2, and α3 polypeptides. The α1 subunit is red, the α2 subunit is blue, and the α3 subunit is in yellow. These α chains are highly polymorphic to allow binding of a wide variety of peptides.
Here, you can view the interior of the MHC class I molecule. Look closely at how the β2 microglobulin associates with the α chains.
The β2 microglobulin associates primarily with the α3 chain, though it does not have a transmembrane region. The α3 chain has a transmembrane domain attached to its carboxyl terminus (not depicted in this molecular representation).
This is another representation of the interior of the molecule.
References
1Madden DR. 1995. The three dimensional structure of peptide-MHC complexes. Annu. Rev. Immunol. 13: 587-622.
2Becker JW and GN Reeke Jr. 1985. Three dimensional structure of β2-microglobulin. Proc. Natl. Acad. Sci. 82: 4225-4229.