FANDOM


A2 growth in PDB

Growth in the PDB database from 1972 to 2006. Structures and complexity have become increasingly more complex with better experimental techniques and technological advancements. Myoglobin atomic structure was originally transferred lab to lab on 1000 single cards, but can now be found online in the PDB database, along with thousands of other macromolecules.


As discussed briefly in the article Structural Bioinformatics , the Protein Data Bank (PDB) is a remarkable asset in structural biology. The PDB is a database of the atomic structure of proteins, and some other macromolecules like nucleic acids, that biologists and biochemists have compiled for the use of other scientists, students and the general public. The primary information stored in this database is called “coordinate files” which show each atom’s spatial location within the three-dimensional structure of the macromolecule. This atomic composition is experimentally generated by methods such as X-ray crystallography, cryo-electron microscopy and NMR spectrophotometry. Accompanying the image of the structure is also the primary sequence, chemistry, functional structure (termed biological assembly) and the function of the macromolecule, if each is known. Often, each macromolecule is accompanied by primary literature or an article written by an expert in the field.

HistoryEdit

The need for a protein database became evident in the early 1970’s as protein crystallography and three-dimensional structure became more advanced and popular within the field of biology. At that time, only a select few laboratories had exchanged coordinates, what is now known as coordinate files, on single cards. This meant that a protein with one thousand atoms required one thousand cards, a very inefficient and complex way of exchanging information. By 1971, Walter Hamilton, a chemist working to determine the structure of amino acids, with the help of other experts in the field established the Protein Data Bank in collaboration with the Cambridge Crystallographic Data Center and Brookhaven National Laboratory. Shortly after in 1974, PDB had 13 structures in its database. Today, the PDB has over 93,000 structures. 


Quick Guide to Using PDBEdit

PDB can be used in two ways:

A2 PDB search

Figure 1: PDB Search Tab. This allows one to search for an author, macromolecule, sequence or ligand within the database.

a) To search for specific macromolecules, sequences or ligands to primarily determine atomic and 3D structure. Here's what happens when I did a basic search: 

I searched for the mammalian target of rapamycin (mTOR) under macromolecules in the search bar shown in Figure 1.This brought me to a page that if I scrolled down, I would find a list of articles related to mTOR. I chose this link as shown in Figure 2. It provided me with information about the article itself, including the location in PubMed , the molecular description and the structural image.

A2 PDB mTOR search

Figure 2: The structure of the rapamycin binding domain of mTOR.

b) To investigate different macromolecules of interest through PDB-101, written in a more relaxed article style immediately relevant to human life (Figure 3). Here one can find interesting current topics in the field such as this month's Molecule of the Month, designed protein cages. If one is interested in the structure of the molecule, it is easy enough to click on the picture and choose the desired image (cartoon, ball and stick, ligans and pocket, etc). In addition, these molecules can also have PDB entries which contain more detailed information on the structure.

Finding proteins in pdb

Finding proteins in pdb.mov

This shows what your computer screen will look like when you are on the PDB website. The narrator shows you the two ways in which you can search for macromolecules.

                       

A2 PDB search PDB101

Figure 3: The homepage of PDB-101. This page has links to articles that may be more relevant to the general person's interests, such as human disease. These are scientific and informative, but usually only a basic background in biology is sufficient to understand the articles. You need not be an expert in structural biology to understand these articles.

                       

                       

                                                                                                                                                                                  


                                                                                                                                                                       

ReferencesEdit

Berman, Helen. "The Protein Data Bank: a historical persceptive". 2007. http://www.ebi.ac.uk/msd/embo08/pdf/pdb_history.pdf

The Protein Data Bank. http://www.rcsb.org/pdb/home/home.do

"The Protein Data Bank". Wikipedia. http://en.wikipedia.org/wiki/Protein_Data_Bank </li>