BioSync is Alive and Growing

link to: biosync.rcsb.org

BioSync (Structural Biology Synchrotron Users Organization) was formed in 1990 as a grassroots organization intended to promote access to synchrotron radiation. It established a web-based clearinghouse for beamline information at synchrotron facilities. The BioSync resource, originally designed and hosted by UCSD/SDSC, has been updated and is now being maintained by the RCSB PDB at BioSync.rcsb.org.

With its bright new look, the BioSync website currently contains updated descriptions of operational US synchrotron beamlines used for single crystal macromolecular crystallography. International sites and beamlines are listed and will go 'live' as data is added for each one. PDB deposition statistics, grouped by site and beamline, are also available.

Future plans for the BioSync site include adding more beamlines for small angle X-ray scattering, X-ray spectroscopy and neutron scattering, and cross linking with the RCSB PDB.

Comments and suggestions are welcome at BioSync@deposit.pdb.org.


RCSB PDB Poster Prize at ACA, ECM, ISMB, and AsCA

The RCSB PDB is pleased to announce the 2006 RCSB PDB Poster Prize, which recognizes student poster presentations at society meetings.

The prize will be awarded to the best posters related to macromolecular crystallography by undergraduate or graduate students at each of the meetings of the IUCr Regional Associates-the American Crystallographic Association (ACA), the European Crystallographic Association (ECM), and the Asian Crystallographic Association (AsCA).

At the Intelligent Systems for Molecular Biology (ISMB), the prize will be awarded to the best student poster in the "Structural Bioinformatics" category.

The awards consist of related educational books, and will be announced through the RCSB PDB website and newsletter. Information about previous winners and awards is available.

The 2005 RCSB PDB Poster Prize winners: Melanie A. Adams at ACA and Sasa Jenko Kokalj at IUCr. (Not pictured: Andrew V. McDonnell and Alexandra Shulman-Peleg, co-winners at RECOMB)

Art of Science Exhibits at UCSD

Featuring images that explore the beauty found in structural biology, the RCSB PDB's Art of Science exhibit was on display with other artworks at Calit2 (University of California, San Diego) from June 9 - 30, 2006.

Molecule of the Month writer and illustrator David S. Goodsell (The Scripps Research Institute) provided additional watercolors, including a cross-section of blood serum, the interaction of HIV in the blood, and an illustration of a eukaryotic cytoplasm.

A wood carving of anthocyanidin synthatase, the natural pigment of berries, fruits and grapes, and a sculpture of human metalloelastase - both by Edgar Meyer (Texas A&M) - were also on display.

The exhibit was located in of the Calit2 building on the UCSD campus, next to the virtual reality visualization lab where "PDB-in-a-CAVE" demonstrations are run. The CAVE offers a room-sized space for users to interact with high-resolution video. Wearing stereoglasses, the viewer can move through and around a projected biological macromolecule.

The Art of Science traveling exhibit includes pictures available from the RCSB PDB website and Molecule of the Month features. Since its beginnings at Rutgers University in New Jersey, the show has traveled to 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.

David Goodsell: http://www.scripps.edu/mb/goodsell/
Edgar Meyer: http://molecular-sculpture.com

Meetings and Exhibits

  • NSTA

    Jeff Milton met with teachers from around the country at the RCSB PDB's exhibit booth at the National Science Teacher's Association 54th National Conference on Science Education (April 6-9 in Anaheim, CA).

  • MAMC

    Annotator Massy Rajabzadeh presented the poster "Depositing Crystal Structures at the RCSB PDB in Five Simple Steps" and met with depositors at the 36th Mid-Atlantic Macromolecular Crystallography Meeting (June 1-3 at Wake Forest University in Winston-Salem, NC).

  • Three-Dimensional Electron Microscopy

    RCSB PDB Director Helen M. Berman described "How the History of the Protein Data Bank can inform the Future of Structural Biology" as one of the Keynote Lectures at the Gordon Conference on Three-Dimensional Electron Microscopy (June 25-30 at Il Ciocco, Barga, Italy).

RCSB PDB Focus: Using Images From the RCSB PDB

The contents of the RCSB PDB are in the public domain. Online and printed resources are welcome to include PDB data and images from the RCSB PDB pages as long as the images are not being sold commercially. It is expected that the corresponding citations are included.

For example, the prepared images available for each structure (from the Structure Explorer pages) should cite the corresponding reference for the entry and the RCSB PDB:

PDB ID: 1di0 B.C.Braden, C.A.Velikovsky, A.A.Cauerhff, I.Polikarpov, F.A.Goldbaum, Divergence in Macromolecular Assembly: X-Ray Crystallographic Structure Analysis of Lumazine Synthase from Brucella abortus, J.Mol.Biol. 297 pp. 1031 (2000). Image from the RCSB PDB (www.pdb.org; H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne, The Protein Data Bank, Nucleic Acids Research, 28 pp. 235-242 (2000))

Pictures from Molecule of the Month features should also credit the illustrator David S. Goodsell of the Scripps Research Institute:

Image of luciferase from David S. Goodsell's (The Scripps Research Institute) Molecule of the Month series at the RCSB PDB (www.pdb.org; H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne, The Protein Data Bank, Nucleic Acids Research, 28 pp. 235-242 (2000); structure shown is 2d1s: T.Nakatsu, S.Ichiyama, J.Hiratake, A.Saldanha, N.Kobashi, K.Sakata, H.Kato, Structural basis for the spectral difference in luciferase bioluminescence, Nature, 440 pp.372-376 (2006))

A full list of related citations is available online.

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 Hemagglutinin, Glucose Oxidase and Luciferase.

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

  • May: Glucose Oxidase

    Diabetes is a worldwide health problem affecting hundreds of millions of people. Fortunately, with careful management of diet and medication, the many complications of diabetes can be reduced. Part of this treatment includes the monitoring of glucose levels in the blood, so that proper action may be taken if levels get too high. The enzyme glucose oxidase has made glucose measurement fast, easy, and inexpensive.

    PDB ID 1gpe: Wohlfahrt, G., Witt, S., Hendle, J., Schomburg, D., Kalisz, H.M., Hecht, H.J. 1.8 and 1.9 A resolution structures of the Penicillium amagasakiense and Aspergillus niger glucose oxidases as a basis for modelling substrate complexes. Acta Crystallogr., Sect.D v55 pp.969-977 (1999)