Step 6: Exploring Protein Sequence and Structure Data

Task(s):  Visually identify sequence variation between IMA1 proteins in our three yeast species, and find the 3D structure of the IMA1 protein for further examination. 

Background on NCBI Resources Used:

NCBI BLAST graphical results options: The web BLAST interface provides many options for visualizing and summarizing the results of a search. Of these, we are going to make the most use of the Alignment and MSA (Multiple Sequence Alignment) viewer options. More about the MSA Viewer, which can be used on its own, can be found starting from the NCBI MSA Viewer landing page. You will use these tools to identify variation between several IMA1 sequences. 

Structure Database: NCBI’s Structure Database stores three dimensional macromolecular structure information. Three dimensional structures provide a wealth of information on the biological function and the evolutionary history of macromolecules. They can be used to examine sequence-structure-function relationships, interactions, active sites, and more. We are going to find and examine a Structure database record for an IMA1 protein.

Macromolecular Modeling Database (MMDB): Experimentally resolved structures of proteins, RNA, and DNA, derived from the Protein Data Bank (PDB), with value-added features such as explicit chemical graphs, computationally identified 3D domains  that are used to identify similar 3D structures, as well as links to literature, similar sequences, information about chemicals bound to the structures, and more. These connections make it possible, for example, to find 3D structures for homologs of a protein sequence of interest, then interactively view the sequence-structure relationships, active sites, bound chemicals, journal articles, and more. The particular IMA1 record we examine will be a experimentally determined crystal structure record from MMDB.

iCn3D: NCBI’s iCn3D, pronounced "I See in 3D", Structure Viewer is a web-based 3D viewer with structure analysis capabilities. The web-based nature of the tool means no downloads are needed to start visualizing and learning! We are going to be using the basics of this tool to start connecting the IMA1 protein structure to its function. 

Basic BLAST Alignment Viewing 

Before we begin, you can make a hypothesis about what variation we might see. Consider what we learned about the biology and genomes of our yeast species - Which protein - the one from S. pastorianus or S. eubayanus - will be more similar to our input S. cerevisiae sequence? 

In this step, we are going to take an initial look at differences between the sequences of our query IMA1 protein (S. cerevisiae), and those from S. eubayanus and S. pastorianus. 

This takes just two steps: 

2. Click on the Alignment tab! 

By default, the alignment output is a plain Pairwise alignment. Each section of the page represents one of the three proteins we selected aligned to the S. cerevisiae sequence.

We can “eyeball” some differences, such as the one I highlighted above, but we can make some adjustments to better spot the differences using the Alignment View Dropdown menu:

Save the Structure record to the Yeast research folder! 1. Click "Send to" to add to the existing Yeast research folder. 3. If it worked you'll see this message  or you can click on your name at the top to go to your Dashboard and see your collection there!

Next, click the associated link to go to into the actual Structure record for the Crystal Structure Of Isomaltase In Complex With Maltose

Once again, this a page with a lotttttt of information. The top part of this page provides some background and information to help you determine if you are on the right page, such as an abstract for the citation related to this MMDB entry.

For a hint about what to look for, click here.

For future work, you could click on any number of download links
(such as those under Download Structure Data) links
to download the data to a folder on your computer!

The molecular components table is also a rich source of information and links out to other databases, and ways to search for similar domains and molecules: 

For more information about how to make sense of all the data on this page, MMDB has an extremely thorough of these pages in their help documentation.

Advanced: Interactive 3d Structure with iCn3D

To see a fully interactive, customizeable version of the chemical structure of IMA1, click on this button!