Tutorial

For this simple tutorial, we will be comparing the Sequence Similarity in 3D of the small ubiquitin-related modifier protein (SUMO-1) and the ubiquitin protein (Ub).

At the end, we will be able to use the SS3D output to generate a matrix and also using as a coloring method when viewing the SUMO-1 pdb structure.

Getting the structure files

The structure of both proteins are present in the PDB data bank at: 1ubq(Ub) and 1a5r(SUMO-1). Download the structure as PDB format and also fasta sequence of the two proteins.

Preparing the file

Looking at the 1a5r.pdb file, we can see that there are 10 different models to represent SUMO-1. We can remove the models from 2 to 10 to facilitate our visualization, leaving only the first model present in the file using a text editor.

Now, we need to align the tertiary structure of the proteins, and remove disordered and high RMSD portions of the proteins. There are many ways to accomplish that, but for this tutorial we used the Matchmaker tool from Chimera software.

We need to align the primary structure of the proteins, and remove the gaps from the pdb file There are many online tools to do so, but for this tutorial we are going to use the EMBOSS Needle, accessible here.

1. Open the link above;
2. For the first protein, click in browse and choose the downloaded fasta file 1a5r.fasta.txt, and then click in open;
3. For the second protein, click in browse and choose the downloaded fasta file 1ubq.fasta.txt, and then click in open;
4. At the end of the page, click in Submit, and wait until the job is finished by the server;
5. We can see that two gaps are present, one at the beginning and other at the end of the sequence. To align the pdb file, we need to remove from 1a5r.pdb the GLY-1 to the TYR21, and the HIS98 to the VAL101.

Running the SS3D analysis

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Generating a matrix visualization

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Mapping the score value to the B-factor

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