• Status Report on "Large Macromolecular Complexes in the Protein Data Bank" Published
  • An overview of the large complexes in the PDB and some of the challenges experienced in their representation, visualization, analysis, and archiving has been published.

    Large Macromolecular Complexes in the Protein Data Bank: A Status Report
    Shuchismita Dutta and Helen M. Berman
    Structure, Vol 13, 381-388, March 2005


  • Biophysical Society
  • RCSB PDB exhibited at the 49th Annual Meeting of the Biophysical Society (February 12-16, 2005) in Long Beach, California. Demonstrations of the beta site were presented.

    Lei Xie prepares to demonstrate the beta site at the Biophysical Society Meeting

Physical Model of February's Molecule of the Month - Major Histocompatibility Complex - Available on Loan to Educators

s part of a project by Molecule of the Month author David S. Goodsell (The Scripps Institute) and Tim Herman (Center for BioMolecular Modeling), a physical model of Class I MHC is available on loan to educators. This study will explore how physical models can be used to enhance the value of the online Molecule of the Month teaching resource. The models may be borrowed for a period of two weeks. The only cost involved is for return shipping. Further information about this opportunity is available at http://www.rpc.msoe.edu/cbm/borrow_mhc.php.


fter working for almost 20 years at CARB and NIST, and serving as a co-director of the RCSB PDB since 1998, Gary L. Gilliland has taken a position with Centocor (a subsidiary of Johnson and Johnson) in Pennsylvania.

Under Gary's leadership, the RCSB PDB team at CARB/NIST was responsible for cataloging, archiving, and preserving the legacy PDB materials that have been accumulating since the PDB was established in 1971 at Brookhaven National Laboratory. This team also distributed data CDs of PDB files worldwide and maintained an exact copy of the RCSB PDB production site which served as both a mirror site and a fail-over system. The functions formerly performed at the CARB/NIST site will now be assumed by the groups at Rutgers and UCSD/SDSC.

The transition has now been successfully completed. The entire RCSB PDB team thanks Gary and wishes him the best of luck in his new adventures in the world of macromolecular structural biology.

PDB MOLECULES OF THE QUARTER: Phenylalanine Hydroxylase, Major Histocompatibility Complex, T-Cell Receptor

he Molecule of the Month series explores the functions and significance of selected biological macromolecules for a general audience.

January: Phenylalanine Hydroxylase. Four molecules of phenylalanine hydroxylase interact to form a tetramer, which is the functional unit for this enzyme. Each molecule in the tetramer is organized into three domains: a regulatory domain, a catalytic domain where the enzyme activity resides and a tetramerization domain that assembles four chains into the tetramer. At the heart of each catalytic domain is an iron ion that plays an important role in the enzyme action. A model structure of the complete enzyme tetramer is shown here. This is composed of two PDB files: PDB entry 2pah, which includes the structure of the catalytic and tetramerization domains of the enzyme, and PDB entry 1phz, which includes the regulatory domain flexibly attached to the catalytic domain.

February: Major Histocompatibility Complex. Viruses are insidious enemies, so we must have numerous defenses against them. Antibodies are our first line of defense. Antibodies bind to viruses, mobilizing blood cells to destroy them. But what happens if viruses slip past this defense and get inside a cell? Then, antibodies have no way of finding them and the viruses are safe...but not quite.

Each cell has a second line of defense that it uses to signal the immune system when something goes wrong inside. Cells continually break apart a few of their old, obsolete proteins and display the pieces on their surfaces. The small peptides are held in the Major Histocompatibility Complex (MHC), which grips the peptides and allows the immune system to examine them. In this way, the immune system can monitor what is going on inside the cell. If all the peptides displayed on the cell surface are normal, the immune system leaves the cell alone. But if there is a virus multiplying inside the cell, many of the MHC molecules carry unusual peptides from viral proteins, and the immune system kills the cell.

March: T-Cell Receptor T-cell receptors, like the one shown here from PDB entry 1tcr, are similar to one arm of an antibody. Like antibodies, they are composed of two chains. The binding site is at the tip of the molecule, and is formed of by several loops of the protein chains. The amino acids in these loops are very different in different T-cell receptors, so they are often called hypervariable loops. Each chain also includes a segment at one end that crosses through the membrane, connecting the receptor to the cell surface. These portions are shown schematically here, since they were removed when the crystal structure was solved.