RCSB PDB at IUCr: wwPDB Booth, Presentations, and More

The new RCSB PDB website, along with tools for deposition, was demonstrated at this year's XX Congress & General Assembly of the International Union of Crystallography (IUCr, August 23 - 31 in Florence, Italy). The exhibit was part of the exhibit stand designed with wwPDB partners MSD-EBI and PDBj.

Several talks were also presented during the Congress, including lead annotator Kyle Burkhardt's "Deposition and Validation using RCSB PDB Tools" as part of the CCP4 Workshop; director Helen M. Berman's "How the RCSB validates PDB Structures" during the microsymposium Improving Structures Using Bioinformatics; and software leader Zukang Feng's "Applications at the RCSB Protein Data Bank" during the COMCIFS Open Commission Meeting on the Current Status and Future Prospects of CIF.

Helen M. Berman gave an overview of the wwPDB at the Round Table on Data Mining chaired by Judith L. Flippen-Anderson. wwPDB representatives Kim Henrick (MSD-EBI), Haruki Nakamura (PDBj), and Philip E. Bourne (RCSB PDB) then showed how their different interfaces can be used to mine the data within the PDB archives.

Philip E. Bourne at the wwPDB Roundtable.

The RCSB PDB Poster Prize was awarded to Sasa Jenko Kokalj for "Proline isomerisation in stefin B: A crucial step towards amyloid fibril formation" by Sasa Jenko Kokalj, Gregor Guncar, Eva Zerovnik, and Dusan Turk (Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, Slovenia). The judging committee was comprised of Maria-Arm´┐Żnia Carrondo (Chair), Carlos Frazao, Ramakumar Suryanarayanarao, Xiao-Dong Su, Edward Mitchell, and Marius Jaskolski.

Poster Prize winner Sasa Jenko Kokalj

mmCIF articles published in new edition of the International Tables for Crystallography (Volume G)

Several articles describing the macromolecular Crystallographic Information File format (mmCIF) and how it is used at the RCSB PDB are in the recently-published International Tables for Crystallography Volume G: Definition and Exchange of Crystallographic Data.

Included in this reference guide for programmers, data managers, and crystallographers are in-depth articles that will aid in the design of interoperable computer applications, including "Classification and use of macromolecular data", "Macromolecular dictionary (mmCIF)", "Specification of the Crystallographic Information File", "The Protein Data Bank exchange data dictionary", "The use of mmCIF architecture for PDB data management", and "Specification of a relational Dictionary Definition Language (DDL2)".

This volume was edited by S.R. Hall, and B. McMahon, and published for the International Union of Crystallography by Springer (Dordrecht, The Netherlands) in 2005. Ordering information is available at journals.iucr.org/iucr-top/it/itg/itg.html.

Molecule of the Month Features Available as Individual PDFs

The Molecule of the Month (MOM) series presents short accounts that describe selected molecules from the PDB. These online chapters are now available as downloadable PDFs that can be easily shared, printed, or incorporated into classroom lessons. Users can download individual MOM features by going to the Molecule of the Month contents page and clicking on the PDF link displayed after the molecule title.

Each installment includes an introduction to the structure and function of the molecule and relates the molecule to human health and welfare. Suggestions for viewing structures on the RCSB PDB website and for additional reading are also provided. Produced and illustrated by David S. Goodsell since 2000, the Molecule of the Month is a proven resource for the classroom.

Previous MOM features have explored structures such as actin, collagen, DNA, green fluorescent protein, ribosome, and transfer RNA.

Molecules of the Quarter

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

  • July: TATA-Binding Protein.

    The enzyme RNA polymerase performs the delicate task of unwinding the two strands of DNA and transcribing the genetic information into a strand of RNA. But how does it know where to start? Our cells contain 30,000 genes encoded in billions of nucleotides. For each gene, the cell must be able to start transcription at the right place and at the right time.
    Specialized DNA sequences next to genes, called promoters, define the proper start site and direction for transcription. Promoters vary in sequence and location from organism to organism. In bacteria, typical promoters contain two regions that interact with the sigma subunit of their RNA polymerase. The sigma subunit binds to these DNA sequences, assists the start of transcription, and then detaches from the polymerase as it continues transcription through the gene. Our cells have a far more complex promoter system, using dozens of different proteins to ensure that the proper RNA polymerase is targeted to each gene. The TATA-binding protein is the central element of this system.

    PDB ID 1cdw: Nikolov, D.B., Chen, H., Halay, E.D., Hoffman, A., Roeder, R.G., Burley, S.K.: Crystal structure of a human TATA box-binding protein/TATA element complex. Proc.Natl.Acad.Sci.USA v93 pp. 4862 (1996)

  • August: Neurotrophins

    Your brain is composed of 85 billion interconnected neurons. Individually, each neuron receives signals from its many neighbors, and based on these signals, decides whether to dispatch its own signal to other nerve cells. Together, the combined action of all of these neurons allows us to sense the surrounding world, think about what we see, and make appropriate actions.
    Remarkably, this complicated structure is formed in nine short months as an embryo grows into a baby. Nerve cells start as typical, compact cells, but then they send out long axons and dendrites, connecting to other cells in the brain or even to entirely different parts of the body. Neurons in the growing brain test the connections with their neighbors, looking for the proper wiring. Half of the neurons are discarded during this process, in areas that get too crowded. The half that remain become the nervous system. Throughout the rest of life, these neurons typically do not reproduce, although they do send out more dendrites to neighboring cells as the nervous system grows or repairs damaged areas.


    PDB ID 1bet: McDonald, N.Q., Lapatto, R., Murray-Rust, J., Gunning, J., Wlodawer, A., Blundell, T.L. New protein fold revealed by a 2.3-A resolution crystal structure of nerve growth factor. Nature v354 pp. 411 (1991)

  • September: Cholera Toxin

    Bacteria pull no punches when they fight to protect themselves. Some bacteria build toxins so powerful that a single molecule can kill an entire cell. This is far more effective than chemical poisons like cyanide or arsenic. Chemical poisons attack important molecules one by one, so many, many molecules of cyanide are needed to kill a cell. Bacterial toxins use two strategies to make their toxins far more deadly than this.

    PDB ID 1xtc: Zhang, R.G., Scott, D.L., Westbrook, M.L., Nance, S., Spangler, B.D., Shipley, G.G., Westbrook, E.M. The three-dimensional crystal structure of cholera toxin. J.Mol.Biol. v251 pp. 563 (1995)