Meetings and Exhibits
- American Crystallographic Association (ACA's) Annual Meeting
The RCSB PDB met with many depositors and users at the ACA's Annual Meeting (July 22 to July 27, 2006; Honolulu, Hawaii). Demonstrations of the RCSB PDB website and deposition software tools were given in the exhibit hall.
RCSB PDB Director Helen M. Berman received the M.J. Buerger Award from the ACA. The award recognizes her lifetime work in the development of information services for the global community of researchers who both produce and use macromolecular structural data. The triennial award was established in 1983 in honor of the crystallographic contributions of Martin J. Buerger, Institute Professor Emeritus of M.I.T. and University Professor Emeritus of the University of Connecticut. The award recognizes established scientists who have made contributions of exceptional distinction in areas of interest to the ACA.
Some representatives images of structures done in the course of Helen Berman's research career (clockwise, starting from the upper left): hydration pattern around a dinucleoside phosphate-drug complex (described in (1)), crystal packing in a structure of a ternary complex among CAP, DNA and aCTD (2), crystal packing of a collagen peptide showing the extensive hydration (3), and a view down the helix axis of a B-DNA helix (4). Image from the summer issue of ACA RefleXions.
- Neidle, S., Berman, H. and Shieh, H.S. (1980) Highly structured water network in crystals of a deoxydinucleoside-drug complex. Nature, 288, 129-133.
- Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y.W., Berman, H.M. and Ebright, R.H. (2002) Structural basis of transcription activation: The CAP-alphaCTD-DNA complex. Science, 297, 1562-1566.
- Bella, J., Brodsky, B. and Berman, H.M. (1995) Hydration structure of a collagen peptide. Structure, 3, 893-906.
- Berman, H.M. (1997) Crystal studies of B-DNA: the answers and the questions. Biopolymers, 44, 23-44.
Prof. Berman received the ACA's Buerger Award
The award was made by ACA President Robert Bau at the Buerger Symposium. The session featured a few of Berman's collaborators, and focused on new and emerging technologies for determining biological macromolecular structures, on how the resultant data is used to further the understanding of molecular function, and on the underpinnings of the bioinformatics framework that makes many of these studies possible.
Participants of the "Structural Biology from all Angles" symposium, from left to right: Jordi Bella (University of Manchester), Robert Bau (ACA), Paula Fitzgerald (Merck Research Laboratories), Helen M. Berman, Judith L. Flippen-Anderson (Chair; RCSB PDB), Stephen K. Burley (SGX Pharmaceuticals), Stephen Neidle (University of London), Wah Chiu (Baylor College of Medicine), and John Westbrook (Rutgers).
- In Silico Analysis of Proteins - Celebrating the 20th Anniversary of Swiss-Prot
As part of the celebration of Swiss-Prot's 20 years of service to the scientific community, RCSB PDB Co-Director Philip E. Bourne presented the lecture "The RCSB PDB - Teaching an Old Dog New Tricks" (July 30 - August 4; Fortaleza, Brazil).
- 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB).
At the ISMB meeting (August 6-10, 2006; Fortaleza, Brazil), the RCSB PDB presented new website features and answered questions regarding new tools and services. At the exhibit booth, visitors saw full demonstration and sample code for accessing data and resources through the RCSB PDB's web services framework.
Art of Science Exhibitions
The Art of Science exhibit was on display at City College, The
City University of New York from August 1-11, 2006. Sponsored by
the Pathways Bioinformatics and Biomolecular Center, the exhibit was opened with a presentation by RCSB PDB Director Helen M. Berman. The exhibit and talk coincided with the Center's bioinformatics workshop for high school students.
The exhibit then traveled to the Hostetter Arts Center at The Pingry School in Martinsville, NJ. This exhibit also featured models from 3D Molecular Designs1. For the past few years, Pingry students in Tommie Hata's and Deidre O'Mara's science classes have been interested in structural biology (see Spring 2004's Education Corner). Their SMART teams (Students Modeling a Research Topic) have visited the RCSB PDB at Rutgers, built three-dimensional models of structures, such as RNA polymerase, and presented their work at Experimental Biology conferences. During September, Pingry students (grades 7-12) were able to explore the structures found in the PDB. Biology and art classes were held in the gallery to look at this interesting intersection of art and science, and to inspire students to create works of their own.
If you would be interested in sponsoring this exhibit at your institution, please let us know at firstname.lastname@example.org.
Art of Science at CUNY
Art of Science at The Pingry School
2006 RCSB PDB Poster Prize
The RCSB PDB Poster Prize was awarded for best student posters related to macromolecular crystallography at ACA and the European Crystallographic Meeting (ECM; August 6 - 11; Leuven, Belgium), and for best student poster in the "Structural Bioinformatics" category at ECM this year. The prize will also be awarded at the Asian Crystallographic Association meeting later this year.
Winners received a subscription to Science and an educational book: their choice of a volume of the International Tables for Crystallography (International Union of Crystallography in conjunction with Springer) for the crystallographic prizes, and Bioinformatics: The Machine Learning Approach (Baldi and Brunak, 2001) for the structural bioinformatics prize.
Many thanks to all of the participants, judges, and organizers.
Thioesterase domain of human fatty acid synthase: structural insights into chain-length selectivity.
Charles W. Pemble (1), Steve J. Kridel(2), Todd T. Lowther(1)
(1) Department of Biochemistry, (2) Department of Cancer Biology, School of Medicine, Wake Forest University, Winston-Salem, NC
Structure of Adeno-Associated Virus 1 to 8.6 Angstrom Resolution by Cryo-Electron Microscopy.
Edward Miller (1), Brittney Gurda-Whitaker (1), Lakshmanan Govindasamy (1), Xiaodong Yan (2), Robert McKenna (1), Sergei Zolotukhin (3), Nicholas Muzyczka (4), Timothy Baker (2), Mavis Agbandje-McKenna (1)
(1) Department of Biochemistry & Molecular Biology, (3) Department of Pediatrics, (4) Department of Molecular Genetics & Microbiology, COM, University of Florida, FL; (2) Department of Chemistry/Biochemistry & Molecular Biology, UCSD, San Diego, CA
Judges: Marc Allaire (Brookhaven National Laboratory), John Badger (ActiveSight), Zygmunt Derewenda - Chair (University of Virginia), Quan Hao (Cornell University), Mariusz Jaskolski (A Mickiewicz University), and Charles Weeks (Hauptman-Woodward MRI)
Organizer: Zongchao Jia (Queen's University)
SdsA1 from P. aeruginosa defines a new mechanistic class of sulfatases
Gregor Hagelüken (1), Thorsten M. Adams (2,3), Lutz Wiehlmann (3), Ute Widow (1), Harald Kolmar (2,4), Burkhard Tümmler (3), Dirk W. Heinz (1), Wolf-Dieter Schubert (1)
(1) Helmholtz Centre for Infection Research, formerly German Research Centre for Biotechnology, (2) University of Göttingen, (3) Medizinische Hochschule Hannover, and (4) Darmstadt University of Technology
Judges: Bohdan Schneider (RCSB PDB and Academy of Sciences of the Czech Republic), Guy Dodson (University of York), Wolf-Dieter Schubert (German Research Centre for Biotechnology), Johann Wouters (University of Namur), Sergei Strelkov (Catholic University of Leuven)
Organizer: Bohdan Schneider
Amino acid solvation structure in transmembrane helices from molecular dynamics simulations
Anna C.V. Johansson and Erik Lindahl, Stockholm Bioinformatics Center, Stockholm University
Judges: Antonio Araújo (University of Brasilia), Rita Casadio (University of Bologna), Paula Kuser Falcăo (Embrapa Informática Agropecuária), Dietlind Gerloff (University of Edinburgh), Reinhard Schneider (European Molecular Biology Laboratory, Heidelberg)
Organizers: Junior Barrera, Fernando Luis Barroso da Silva, and Phil Bourne
New RCSB PDB Flyers Available in Print and Online
Two new brochures are available for RCSB PDB users.
The General Information trifold provides an overview of the RCSB PDB project, and includes information about data deposition, data query and reporting, Molecule of the Month, structural genomics, wwPDB, and outreach and education resources.
5 Easy Steps for Structure Deposition describes the tools that facilitate NMR and X-ray crystal structure deposition and validation for use by the authors of the structures.
To receive printed copies of these flyers, please send your postal address and brochure request to email@example.com. Requests can be made for multiple copies.
Molecules of the Quarter
Molecule of the Month series explores the functions and significance
of selected biological macromolecules for a general audience.
The molecules featured this quarter were amyloid-beta precursor protein, AAA+ proteases, and elongation factors.
The complete Molecule of the Month features are accessible from the RCSB PDB home page.
August: AAA+ Proteases
How would you make a protein cutting machine that would be safe to use inside a cell?
Digestive proteases like
are small and efficientthey diffuse up to
proteins and start cutting. This would never work inside a cell. The cell needs to have
more control, so that only obsolete or damaged proteins are destroyed. The AAA+
proteases are one solution to this problem. They use two tricks to ensure that only certain
proteins are destroyed. First, they hide the protein destruction machinery inside a closed
container, and second, they use a special protein pump to feed proteins into this
PDB ID 1yyf: Wang, J., Rho, S.H., Park, H.H., Eom, S.H. Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects. ACTA CRYSTALLOGR.,SECT.D v61 pp.932-941 (2005)