MHC I from Chicken (PDB: 4g42)
Ioannis Tsiligkaridis and Nancy Boury
Most immunology and microbiology textbooks include a figure of major histocompatiblity complex I. This molecule is found on all nucleated vertebrate cells and presents foreign antigen to CD8+ T cells. Most of these figures look something like this:

 

 

 

 

 

However, the three dimensional structure of MHCI is significantly different from the simple line drawing shown in textbooks.

This is the PDBe view of molecule 4g42, with the beta-2 microglobulin displayed as the blue and magenta regions with MHC I the red and green regions showing the MHC I alpha chains. The 3-D structure is considerably more realistic.
Visualizing the 3-D structure from PDBe, using AstexViewer, we can measure the distance between two points. For example, it is 10.93 Angstroms between the carbons in the backbone of the pink beta-sheet shown above. In the AstexView, we can also determine the distances between multiple points in the molecule.

Using Consurf, the MCH I molecule A chain is one of the molecules in the Consurf gallery. Looking at molecular map, showing conserved and non-conserved regions of the molecule, we can see that the area where the A chain interacts with Beta2-microglobulin is well conserved. The outer regions (top of molecule in view shown) of the molecule, however, are more variable. There is also a di-sulfide bridge that was revealed in Consurf that was not evident in Jmol using the Astex viewer.

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