This Week on the PDB: An Introduction

Protein functions are largely dependent on their 3D structure, but where can we find these structures, and more importantly, manipulate them? The answer: The Protein Data Bank (PDB).

The original PDB was established in 1971, and contained a total of seven structures. Since then, it has grown to contain more than 133759 structures. Though the name suggests that only proteins are covered, the scope off the PDB is much wider than just polypeptides. Ligand-bound proteins, nucleic acid-bound proteins, viruses, ribosomes, and just about any other kind of macromolecules can be found on the PDB.

The PDB has a built-in 3D structure viewer accessible through a browser. Using the 3D viewer, you can spin the structure in any direction to get a full 360o view, zoom in, and zoom out. You can also view structures in different styles such as cartoon or ball-and-stick, and you can see the plot of the surface as well. Other features include the amino acid sequence of the protein and seeing how specific residues interact with ligands.

PyMol
An alignment made in PyMol, with sequence view turned on.

The PDB’s built-in viewer has all the features needed for a cursory glimpse of the structure, but lacks features required to do in depth structural analyses. As such, most people tend to download the .pdb file of the structure and view it in another program. The PDB is so ubiquitous in structural biology that structural analysis programs such as PyMol can fetch PDB files just using the 4-digit alphanumeric code associated with a given protein, called the PDB accession code.

Most of the structures on the PDB are obtained through x-ray diffraction, but other techniques, such as electron microscopy, can be used to solve for the structures. There is also a database specifically for structures solved from electron microscopy called the EMDataBank, which is easily accessible from the PDB. The reverse also applies.

Though the PDB contains an immense database of protein and other macromolecular structures, there are still an extraordinary number of macromolecules that have yet to be catalogued. Consequently, the PDB updates once a week, adding newly solved, never-before seen structures.

PDB intro
The main page of the Protein Data Bank.

Now that you have been primed on what the PDB is and how it can be used, I would like to introduce a new column on The Abstract: “This Week on the PDB”! Every week we will present to you the new structures in the PDB, and a short summary of their purpose. Together, let us explore the cutting-edge science of structural biology.

Check out the PDB here: https://www.rcsb.org/pdb/home/home.do

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