RCSB PDB's 2005 Annual Report Now Available

The RCSB Protein Data Bank's Annual Report, which covers the period of July 1, 2004 - June 30, 2005, is currently being distributed.

This snapshot of the RCSB PDB is intended to provide background information about the resource and describe recent progress and accomplishments. Available online as a PDF, this report describes the many different activities in data deposition, data access, and education and looks at the features of the new site.

If you would like a printed copy of the report, please send mail to info@rcsb.org.


Workshop for High School Teachers and Students: Building Protein Models at the Science Olympiad

"Protein modeling" – where students build physical 3D models of proteins – will be a trial event at the Northern Regional and State Final 2006 Science Olympiads in New Jersey.

This event will challenge high school students to explore structure and the relationship of structure to protein function using computer visualization and physical modeling tools. Students are introduced to the resources of the RCSB PDB, learn how to use RasMol, and create protein structures using 'Mini-Toobers' from 3D Molecular Designs.

The RCSB PDB team will be judging the models at the Olympiad and providing the materials for the event.

A training workshop was held at the RCSB PDB at Rutgers, The State University in Piscataway, NJ on Wednesday, December 7, 2005. Tim Herman (MSOE Center for BioMolecular Modeling, www.rpc.msoe.edu/cbm) demonstrated how the Mini-Toobers are used to generate protein model in the competition.

Further details about this workshop and event are available at http://education.pdb.org/olympiad/.

Teachers and students practiced making protein models in preparation for the Science Olympiad.

RCSB PDB Exhibit, Workshop for New Jersey Science Teachers

Teachers examined the three-dimensional structure of biologically important macromolecules at the as part of the RCSB exhibit booth at the New Jersey Science Conference (October 5-6, 2005 in Somerset, NJ). The conference was co-sponsored by the New Jersey Science Teachers Association and the New Jersey Science Education Leadership Association. Two formal workshops were held in preparation for the protein modeling event at the Science Olympiad. At these meetings, Shuchismita Dutta presented "Seeing is believing but meeting is better" to introduce the educational resources of the RCSB PDB to science teachers. Gary Graper (Event Supervisor, Wisconsin Science Olymipad) and Jennifer Morris (Center for BioMolecular Modeling) gave hands-on demonstrations to show how the protein modeling event will work at the Science Olympiad.

Molecules of the Quarter

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

The molecules featured this quarter were Designer Proteins, Acetylcholine Receptor, ATP Synthase.

The complete Molecule of the Month features are accessible from the RCSB PDB home page.

  • October: Designer Proteins.

    As we learn more and more about proteins and how they work, we naturally have the desire to use this knowledge and do some tinkering of our own. Since the early 1980's, scientists have been using the ever-expanding understanding of protein structure and function to redesign existing proteins, and more recently, to design entirely new proteins.

    PDB ID 1qys: Kuhlman, B., Dantas, G., Ireton, G.C., Varani, G., Stoddard, B.L., Baker, D. Design of a Novel Globular Protein Fold with Atomic-Level Accuracy Science v302 pp.1364-1368 (2003)

  • November: Acetylcholine Receptor

    Nerve cells need to be able to send messages to each other quickly and clearly. One way that nerve cells communicate with their neighbors is by sending a burst of small neurotransmitter molecules. These molecules diffuse to the neighboring cell and bind to special receptor proteins in the cell surface. These receptors then open, allowing ions to flow inside.


    PDB ID 2bg9: Unwin, N. Refined Structure of the Nicotinic Acetylcholine Receptor at 4A Resolution J.Mol.Biol. v346 pp.967 (2005)

  • December: ATP Synthase

    ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an indispensable role in our cells, building most of the ATP that powers our cellular processes. The mechanism by which it performs this task is a real surprise.

    Large, complex molecular machines like ATP synthase pose difficult problems for structural scientists, so the structures of these machines are often determined in parts. The picture shown here is a composite of four different structures, combining structures determined by X-ray crystallography and NMR spectroscopy.

    PDB ID 1e79: Gibbons, C., Montgomery, M.G., Leslie, A.G., Walker, J.E. The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution. Nat.Struct.Biol. v7 pp.1055-1061 (2000)
    PDB ID 1c17: Rastogi, V.K., Girvin, M.E. Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature v402 pp.263-268 (1999)
    PDB ID 2a7f: Wilkens, S., Borchardt, D., Weber, J., Senior, A.E. Structural Characterization of the Interaction of the delta and alpha Subunits of the Escherichia coli F(1)F(0)-ATP Synthase by NMR Spectroscopy Biochemistry v44 pp.11786-11794 (2005)
    PDB ID 1l2p: Del Rizzo, P.A., Bi, Y., Dunn, S.D., Shilton, B.H. The "second stalk" of Escherichia coli ATP synthase: structure of the isolated dimerization domain. Biochemistry v41 pp.6875-6884 (2002)