Protein Data Bank (PDB)

Assalamualaikum wr, wbt..,

Today"s lecture is about PDB (Protein Data Bank). Actually it is a resource for scientist for studying biological macromolecules. It  is an interesting topic to be learned.The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. The RCSB PDB also provides a variety of tools and resources. We can perform simple and advanced searches based on annotations relating to sequence, structure and function. These molecules can be visualized, downloaded, and analyzed.

Below, there is link for us to know the detail about PDB.......

http://www.pdb.org/pdb/home/home.do 

http://en.wikipedia.org/wiki/Protein_Data_Bank

For example, the picture showed the structure of Lon ATP-dependent Proteases  that we can get from PDB website. The explanation about the enzyme is written the table below. ( actually it is just COPY & PASTE.... huhu). By the way, is just an example.. So take it easy...........

Lon ATP-dependent proteases

Lon ATP-dependent proteases are key components of the protein quality control systems of bacterial cells and eukaryotic organelles. Eubacterial Lon proteases contain an N-terminal domain, an ATPase domain, and a protease domain, all in one polypeptide chain. The N-terminal domain is thought to be involved in substrate recognition, the ATPase domain in substrate unfolding and translocation into the protease chamber, and the protease domain in the hydrolysis of polypeptides into small peptide fragments. Like other AAA+ ATPases and self-compartmentalising proteases, Lon functions as an oligomeric complex, although the subunit stoichiometry is currently unclear. Here, we present crystal structures of truncated versions of Lon protease from Bacillus subtilis (BsLon), which reveal previously unknown architectural features of Lon complexes. Our analytical ultracentrifugation and electron microscopy show different oligomerisation of Lon proteases from two different bacterial species, Aquifex aeolicus and B. subtilis. The structure of BsLon-AP shows a hexameric complex consisting of a small part of the N-terminal domain, the ATPase, and protease domains. The structure shows the approximate arrangement of the three functional domains of Lon. It also reveals a resemblance between the architecture of Lon proteases and the bacterial proteasome-like protease HslUV. Our second structure, BsLon-N, represents the first 209 amino acids of the N-terminal domain of BsLon and consists of a globular domain, similar in structure to the E. coli Lon N-terminal domain, and an additional four-helix bundle, which is part of a predicted coiled-coil region. An unexpected dimeric interaction between BsLon-N monomers reveals the possibility that Lon complexes may be stabilised by coiled-coil interactions between neighbouring N-terminal domains. Together, BsLon-N and BsLon-AP are 36 amino acids short of offering a complete picture of a full-length Lon protease.

tHAT'S ALL, THANK YOU.....


WASSALAM