Exercises on Protein Structure

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Go to parent Basic bioinformatics concepts, databases and tools#Exercises_during_the_training

The PDB database

PDB (Protein Data Bank at http://www.rcsb.org/) is a database of experimentally determined 3D-structures of nucleic acids, proteins and their complexes. It is maintained by the Research Collaboratory for Structural Bioinformatics (RCSB). The structures have been determined by X-ray diffraction (on crystalized proteins) or NMR (on proteins in solution).

Exercise 1

Retrieve the structure for the human VH-1-related phosphatase (1VHR).

  • go to http://www.rcsb.org/
  • enter 1VHR in the search term box. Just like on the NCBI home page, it's a simple text box in which you can type PDB-IDs or keywords
  • click Go button

More detailed search options, such as Advanced Search are available below the search box.


For structure information and search results, tabs can be used to toggle between different topics.


As said before PDB is highly redundant. In an attempt to remove the redundancy sets of highly similar structures were replaced by a single representative. In our case that representative is 3F81.A

However, you need a more detailed overview of the secondary structure than what you see here.

VAST+, the enhanced version of VAST, short for Vector Alignment Search Tool, is a computer algorithm developed at NCBI and used to identify similar protein 3D structures by purely geometric criteria to identify distant homologs that cannot be recognized by sequence comparison.

The ninth hit with PDB ID 3F81 is a copy of 1VHR in the NCBI structure database. You can see that this is a copy by clicking the ID on the VAST results page. This opens the record of 3F81 where you can see that 3F81 is VHR. The third hit with ID 1J4X is also a copy of VHR, in which a single mutation was introduced.

View the structure of the protein in YASARA. This software is already installed on the BITS laptops: click on the YASARA icon on the desktop to open the software.

Handicon.png Before you start using YASARA, view the Working with YASARA movie to make you familiar with the user interface.
In YASARA go to: Help > Play help movie > General: Working with YASARA

YASARA can automatically fetch files from PDB:

  • File > Load > PDB file from Internet
  • enter "1VHR" in the "PDB ID" box
  • select "Download" "from www.RSCB.org (official structure)"
  • click "OK"

Now do the same for 1VHR and 4B04: you will see that the alignment is not so nice.

Exercise 2

Find the structures of bHLH (basic helix-loop-helix) proteins in PDB. These proteins bind DNA and are involved in the regulation of gene expression.

You do not have to use a PDB ID to search PDB, you can also use keywords. Search PDB for "bhlh". In the left menu you will get an overview of ways to refine your query. Below you see a list of 26 PDB records that contain the word "bhlh".

We are looking for a yeast bHLH so use the Organism Refinements to filter the results for Saccharomyces cerevisiae bHLH structures. This takes you to the record of 1A0A.

Check the Structure Summary tab. The "Experimental Data Snapshot" section shows the method to solve the 3D structure, the resolution, and the overall quality of the structure (R free value).


Look at the detailed quality description with the sliders.

You can download the full quality report by clicking the figure.

This will save the file in your Downloads folder. Open the PDB file in a text editor like WordPad.

In YASARA, you can also load structures from a PDB file on your computer.

  • File > Load > PDB file
  • Scroll to the file on your computer, select it
  • Click "OK"
  • Remove all waters
  • Rotate, move and zoom out to fit the structure on your screen
  • Select an amino acid by clicking it and see which amino acid you've selected in the "Sequence" bar at the bottom of the YASARA window.


    Additional exercises

  • Uniprot / PDB exercises: Exploring_the_Protein_Data_Bank_exercises
  • YASARA exercises: