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XI.D. PyMOL Superimposition

Roderico Acevedo and Kristen Procko

Overview: This activity demonstrates how to align two objects in the modeling program.

Outcome: The user will be able to superimpose two similar macromolecules to examine commonalities and differences.

Time to complete: 5 minutes

Modeling Skills

  • Superimposing objects

About the Models

PDB ID: 1xww & 5pnt (different isozymes)

Protein: Low molecular weight protein tyrosine phosphatase

Activity:  Hydrolyzes Tyr-OPO32-  phosphoester bond

Description:  Single chain, bound SO42- competitive inhibitor, bound glycerol (nonspecific stabilizer)

Note: We will be using the command super for superimposing two isozymes. PyMOL has three different commands to accomplish this task: align, super, and cealign. Briefly, align is recommended for structures that have high sequence similarity, while super is a sequence-independent command useful for structurally similar macromolecules. The command cealign is recommended for low sequence identity macromolecules. For more detailed information, please consult the PyMOL wiki page on superimposition.

Steps

  1. Fetch the two structures. In the command line, type: fetch 1xww 5pnt, type=pdb1
  2. Apply the superimpose command. In the command line, type: super 1xww, 5pnt
The left panel shows a rendering of cartoon mode for two proteins before superimposition with one protein shown in turquoise and the other in green. The right panel shows the same proteins after they are superimposed.
Figure 1: Before and after snapshot of using the alignment command (super)

Note: The first structure moves to superimpose onto the second structure.  If you wish for 1xww to remain in the same position, type: super 5pnt, 1xww

 

 

  1. Select a 5 Å zone around MES (2-(N-Morpholino)-ethanesulfonic acid) and display those residues as sticks. It may be helpful to hide the cartoon backbone of the two proteins.
    Rendering of two superimposed proteins (cpk with green carbons and cpk with cyan carbons) in the active site shown as colored sticks.
    Figure 2: Only active site residues are shown, as colored sticks.

 

What differences can you see between the active sites of the proteins?

 

 

Video Tutorial

Here is a video on superimposition in PyMOL (especially for when the super command doesn’t work well).

Click here to go to Chapter XII: Mutagenesis

License

Seeing the Invisible: Learning to Teach with Biomolecular Visualization Copyright © by The BioMolViz Working Group. All Rights Reserved.

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