BCB 444/544 Fall 06 Oct. 4th Lab 6 p. 1
BCB 444/544
Lab 6 Name _____________________________
Macromolecular Structure Visualization
Objectives
1. Learn about the protein structure resources available at the PDB and NCBI
2. Understand the portions of a PDB formatted structure file relevant to structure visualization
3. Learn to use some useful features of the structural visualization programs, PyMol and Cn3D
Introduction
“The Protein Data Bank (PDB) is the single worldwide depository of information about the three-dimensional
structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life
that are found in all organisms including bacteria, yeast, plants, flies, and mice, and in healthy as well as
diseased humans. Understanding the shape of a molecule helps to understand how it works.”
This introduction from the PDB provides the motivation for today’s exercises. In order to better understand a
particular protein, it is important to be able to retrieve structures of interest from the PDB, and to be able to
manipulate how these structures are displayed in order to highlight regions of interest.
Exercises
Required questions are in red.
Note: If you were not able to attend the regularly scheduled lab section, it may help to review the background
lecture slides, which can be downloaded from the course webpage. Please feel free to ask a TA if you have any
questions regarding these slides.
*Certain features of PDB require popups, so you may need to turn off popup blocking for the time being.
Please ask a TA if you need help with this.
1) Querying the PDB (Protein Data Bank) To familiarize yourself with the PDB website, start by
viewing the PDB tutorial at: http://www.pdb.org/pdbstatic/tutorials/Main_Tutorial.swf We will now
practice querying the PDB using the dystrophin protein discussed in our previous lab on NCBI
resources.
a. Open your web browser, and enter http://pdb.org in the address bar
b. We will start with a simple keyword query. In the search bar, type dystrophin, then hit enter.
How many structure hits were found by this query? To narrow down the list of structures, we
will utilize the advanced search function of the PDB.
c. In the left menu, click on the Search tab, then click Search Database, then click Advanced
Search. Click on the “Choose a Query Type:” dropdown menu to bring up the list of available
queries. We will not be using most of these, but it is good to be aware of what is available, so
take a second to scroll down the list. Go back near the top of the list and select “Molecule Name”
under the “Structure Summary--” subheading. Type dystrophin in the box, then click Evaluate
Subquery. This feature will tell us how many structures would be returned by this particular
query. How many structures were found by this query?
d. Click Evaluate Query to view these results. We now see that the first result is the N-terminal
domain of dystrophin, with id: 1DXX. We will return to this structure in a moment, using the
Queries tab in the left menu to return to this query. For now we will perform a new query that
provides a better example of how you might use advanced search to obtain a set of proteins with
a desired property, rather than searching for one specific protein. In this example, let’s say we
want to find all structures of nucleic acid-binding proteins in which the protein is not currently
bound to nucleic acid.
