Try it! – Align multiple structures using jFATCAT

This tutorial demonstrates how to align two structurally homologous protein files within a single document. This technique is useful for discovering similarities and differences between related structures. The files used in this tutorial will be opened from the RCSB Protein Data Bank (PDB) using the Protean 3D interface:

• 1BFD – The crystal structure of benzoylformate decarboxylase. We will use chain A from this structure.

• 1PVD – The crystal structure of pyruvate decarboxylase. We will use chain B from this structure.

These two proteins exhibit structural homology, although they have only a 19% sequence identity. Their structural homology may indicate either distant sequence homology or convergent evolution.

1. Launch Protean 3D and choose Open Project on the left and Open from PDB on the right. Type in 1BFD and click OK.
   
   

2. Choose Structure > Align Structures > Structure Alignment. The wizard opens at the Structure screen. Note the the PDB fie you added in the previous step is already in the Files list.

3. Click the Add PDB ID button, type 1PVD into the text box, and click OK. Now that both structures have been added, the Structure screen now looks like the image below.
   
   
   
   Click Next to proceed to the Selection screen.

4. In the Selection screen, the whole structures appear on the right.
   
   
   
   However, we don’t want to align both structures; one of which has a single chain, and the other of which has two chains. We only want to align chain A of one structure and chain B of the other structure. To make those choices:
   
   
   1. Use Shift+click to select both items on the right and press the blue “left” arrow to remove them from the “Display columns” list.
      
      
   2. Use Ctrl/Cmd+click to select 1BFD:A and 1PVD:B from the list on the left. Press the blue “right” arrow to move them to the “Display columns” list.
      
      
   3. Leave the Target at the default of 1BFD:A. The screen now appears as follows.
      
      

5. Press Run Now to initiate the structure alignment using the default alignment algorithm of jFATCAT. (If we had wanted to use TM-Align, we could have clicked next to proceed to the Alignment screen and chosen it there before running).

6. To facilitate the structure comparison, we can now color the two structures by chain. Choose View > Style > Color to open the Color bar. From the Color Style drop-down menu, select Color by chain.
   
   
   
   The Structure view image now appears as below.
   
   
   
   Note that even though we told Protean 3D which two chains to compare, all three chains appear in the image.
   
   
   • 1BFD chain A is colored in green.
     
   • 1PVD chain B is colored in blue and aligns well with the green chain above.
     
   • 1PVD chain A is colored in yellow, and does not overlap with the others.

7. To hide display of the extraneous yellow chain (optional), use View > Explorer > Molecules and remove the checkmark next to 1PVD > A.

8. In the Report view, look at the RMSD value in Report 2, which is 3.342 Å.
   
   
   
   RMSD quantifies the degree of similarity by describing the average distance, in Angstroms (Å), between the atoms of two superimposed structures. The RMSD value is inversely proportional to the degree of similarity between the structures. As a very general rule of thumb:
   
   
   • RMSD ≤ 0.5 Å indicates near-identical structural similarity.
     
   • RMSD between 0.5-2.0 Å corresponds to a high degree of similarity.
     
   • RMSD between 2.0-5.0 Å indicates a lower, but still noticeable, degree of similarity.

The RMSD of 3.342 Å is compatible with our knowledge that the two sequences have a 19% sequence identity.