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For answers to questions ranging from "how can I deposit my structure" to "how can I create a report about the structures I've found" to "what is DNA?", the RCSB PDB actively maintains several e-mail help desks. Responses are rapidly returned.


  • Art of Science Exhibit at Texas A&M and Rutgers

    The RCSB PDB's "Art of Science" exhibit was on tour this past spring. It appeared at Texas A&M University's Visual Arts Gallery in the Memorial Student Center (April 13 - May 15, 2005). The show was also part of the American Chemical Society Mid-Atlantic Regional Meeting (MARM) held at Rutgers (May 22-25, 2005).

    The Art of Science traveling exhibit looks at the beauty inherent in protein structures. It displays images of molecules in the PDB, including the pictures available from Structure Explorer pages and from Molecule of the Month features. Since its beginnings at a space dedicated to art exhibits at Rutgers University, the show has traveled to many places, including EMBL-Hamburg, Germany; University of Wisconsin-Madison; California State University, Fullerton; Purdue University; and Hyderabad, India. The RCSB PDB would like to see the "Art of Science" travel to other places. If you would be interested in sponsoring this exhibit at your institution, please let us know at info@rcsb.org.

  • RCSB PDB Educational Resources Poster

    Resources for education available from the RCSB PDB are highlighted on a poster that is available for download (www.rcsb.org/pdb/education.html; 8 1/2 by 11 inches).

    • The Molecule of the Month feature illustrates important biological molecules and how they function through descriptive text, pictures, and links to specific PDB entries and other resources.

    • The RCSB PDB Newsletter regularly features interviews with members of the community and descriptions of how the PDB is used in all levels of education.

    • The Education Page provides resources for learning about Proteins and Nucleic Acids, protein documentaries, and suggested reading materials and links.

    • RCSB PDB tools for finding and visualizing proteins are used in the classroom in a variety of ways, including downloading molecular images, exploring the links to information found in journals, and trying different keyword queries to locate specific proteins.
  • RCSB Meetings: ACA and ISMB

    Highlights from the Annual Meeting of the American Crystallographic Association (ACA) held May 28 - June 2, 2005 in Orlando, FL included exhibiting in "Data Alley", along with CCP4 and CCDC. RCSB PDB staff were on hand to answer questions and provide demonstrations of deposition software and the beta site. Annotator Kyle Burkhardt presented a tutorial on using RCSB PDB validation software at the "Workshop on Macromolecular Structure Validation."

    The RCSB PDB also exhibited at the 13th Annual Meeting of the International Society for Computational Biology ("Intelligent Systems for Molecular Biology" June 25 - 29 in Detroit, Michigan). Wolfgang Bluhm presented "Structural Bioinformatics Education from the RCSB Protein Data Bank" as part the Education session.

  • RCSB Poster Prize awarded at RECOMB and ACA

    Thanks to the students and judges who participated in the recent RCSB PDB Poster awards. Details are available at www.rcsb.org/pdb/poster_prize.html. The next award will be presented at the XX Congress of the International Union of Crystallography (August 23-31 2005 in Florence, Italy).

    • At the Ninth Annual International Conference on Research in Computational Molecular Biology (RECOMB, May 14-18, Cambridge, MA), the RECOMB & PDB Poster Awards recognizing insight and innovation in structural computational biology went to "Comparative Modeling of Mainly-Beta Proteins by Profile Wrapping" by Andrew V. McDonnell, Matthew Menke, Nathan Palmer, Jonathan King, Lenore Cowen, Bonnie Berger (MIT) and "MAPPIS: Multiple Alignment of Protein-Protein Interfaces" by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov and Haim J. Wolfson (Tel-Aviv University).

    • At the ACA, the award for best student presentation went to "Safety in Cycling: Novel Redox Proteins from Escherichia coli" by Melanie A. Adams (pictured) and Zongchao Jia (Queen's University).

Molecules of the Quarter

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

  • April: Kinesin

    Kinesins are used for many tasks in cells. Typical cells contain an array of microtubules, all pointed from the center of the cell outwards to the surface. Kinesins are used to drag large objects, like lysozomes or endoplasmic reticulum, outwards away from the nucleus and towards the surface. Dyneins are used for the opposite function, to pull things inwards. Kinesins drag materials down the enormous length of nerve axons--this function is how kinesins were discovered. Kinesins are also used to slide microtubules next to one another, for instance, during the process of creating two separate systems of microtubules to separate chromosomes when the cell divides.

    PDB ID 3kin: Kozielski, F., Sack, S., Marx, A., Thormahlen, M., Schonbrunn, E., Biou, V., Thompson, A., Mandelkow, E. M., Mandelkow, E.: The crystal structure of dimeric kinesin and implications for microtubule-dependent motility. Cell 91 pp. 985 (1997)

  • May: Self-splicing RNA.

    In plants and animals, most RNA molecules are made as long precursors that need to be trimmed and reassembled to create the final active molecule. These precursor RNA molecules are composed of exons, which are the important parts, separated by introns, which must be removed. In most cases, the RNA is cut and spliced together by a spliceosome, a molecular machine composed of protein and RNA. In a few cases, however, the RNA can perform the splicing reaction on its own. The first example, discovered by Thomas Cech, was a ribosomal RNA found in a protozoan. Since then, hundreds of examples have been identified in genome sequences of many organisms. The example shown here, from PDB entry 1u6b, is part of a bacterial transfer RNA that must be spliced before it can adopt its functional form. In the illustration, the large structure in green is the intron, which uses a GTP and two magnesium ions to remove itself. The two exons that will be spliced together are colored red and blue--note that only a small piece of each exon is included in the structure.


    PDB ID 1u6b: Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J., Strobel, S. A.: Crystal Structure of a Self-Splicing Group I Intron with Both Exons. Nature 430 pp. 45 (2004)

  • June: Carotenoid Oxygenase

    The bright color of carrots and many other orange and yellow vegetables is caused by carotenoid molecules such as beta-carotene. Carotenoids are long, thin molecules with a string of carbon-carbon double bonds in a row. These bonds absorb light and give carotenoids their characteristic yellow color. Hundreds of different types have been discovered in different plants, where they color flowers, leaves, fruits, and even the roots. Carotenoids are remarkably useful, both for the plant and for the people eating the plant. In plants, carotenoids assist the chlorophyll molecules that absorb light in photosynthesis. Carotenoids also absorb excess light when it reaches dangerous levels. Our retinas contain carotenoids such as lutein that protect us from excess light that might damage our eyes. Carotenoids also are antioxidants that scavenge reactive forms of oxygen, destroying them before they damage our molecular machinery.

    PDB ID 2biw. Kloer, D. P., Ruch, S., Al-Babili, S., Beyer, P., Schulz, G. E.: The Structure of a Retinal-Forming Carotenoid Oxygenase Science 308 pp. 267 (2005)