Thanks to the students and judges who participated in the RCSB Poster Prize competitions during this past quarter. The prize is designed to recognize student poster presentations involving macromolecular crystallography. The award was Biochemistry - Vol. I by Donald and Judith G. Voet and Introduction to Macromolecular Crystallography by Alexander McPherson.

Conference of the Asian Crystallographic Association (AsCA; June 27-30; Hong Kong, China). The prize was awarded to Chin-Yu Chen for "Probing the DNA Kink Structure Induced by the Hyperthermophilic Chromosomal Protein SAC7D Using Site-Directed Mutagenesis and X-Ray Crystallography"

Chin-Yu Chen(a-c), Ting-Wan Lin(a), Chia-Cheng Chou(a,b), Tzu-Ping Ko(a), and Andrew H.-J. Wang(a,d)

(a)Institute of Biological Chemistry and (b)Core Facility X-ray Crystallography, Academia Sinica, Taipei 115, Taiwan; (c)Department of Chemistry and (d)Institute of Biochemical Sciences, National Taiwan University, Taipei 106, Taiwan.

The AsCA Judging Committee as organized by Peter Colman - TP Singh and Se Won Suh.

American Crystallographic Association's Annual Meeting (ACA; July 17-22; Chicago, IL). The prize was awarded to Ty Adams for "The Crystal Structure of Factor Va: A New Mechanism for Membrane Binding and Function"

T.E. Adams(a), M.F. Hockin(b), K.G. Mann(a), S.J. Everse(a)

(a)College of Medicine, University of Vermont, Burlington, VT 05401 (b)Howard Hughes Medical Institute, University of Utah, Salt Lake City, UT 84112.

ACA Judging Committee as organized by Edward J. Collins - Jung-Ja Kim (Chair), Richard Brennan, Carolyn Brock, John Chrzas, and Nick Sauter.

22nd European Crystallographic Meeting (ECM 22; August 26-31; Budapest, Hungary). The prize was awarded to Jacques-Ph. Colletier for the poster "Kinetic crystallography on the cholinesterases"

J.P. Colletier(a), A. Royant(b), A. Specht(c), F. Nachon(d), G. Zaccai(a), M. Goeldner(c), J.L Sussman(e), I. Silman(f), D. Bourgeois(b), and M. Weik(a)

(a)LBM & (b)LCCP, IBS, Grenoble, France; (c)LCB, ULP, Strasbourg, France; (d)UE, CRSSA, La Tronche, France; (e)DSB & (f)DNB, WIS, Rehovot, Israel).

ECM 22 Judging Committee - Matthias Bochtler, Zsolt Bocskei, Stefania Di Marco, Andrea Hadfield, and the Chair, Vilmos Fulop.

The RCSB PDB Poster Prize contest will resume in 2005 - further details will be announced in RCSB PDB web site news.


EMBL-Hamburg hosted the conference "Structural Biology at Crossroads: From Biological Molecules to Biological Systems" on September 15-18. An exhibition of the RCSB PDB's Art of Science gallery show was opened during the second evening of the meeting with a presentation by RCSB PDB Director Helen M. Berman. Some of the best movies from the protein structure world were also shown.

The exhibit was on display in the DESY Bistro (Notkestr. 85, Hamburg, Germany) until October 03, 2004.


A paper describing structural genomics' effects on the PDB's data pipeline, data capture, and target tracking has been published in the American Journal of PharmacoGenomics:

The Impact of Structural Genomics on the Protein Data Bank
Helen M. Berman and John Westbrook
Am. J. Pharmacogenomics 2004; 4:247-252


Two products were distributed for the July 2004 data CD release. Release 109U contains the incremental set of experimentally determined structures and models released between April 1, 2004 and July 1, 2004, and release 108U-EXP contains the experimental data (X-ray structure factors and NMR constraints) released during the same quarter. Each is on a single CD-ROM. Questions should be directed to pdbcd@rcsb.org. Ordering information is available at http://www.rcsb.org/pdb/cdrom.html.


The Molecule of the Month series, by David S. Goodsell, explores the functions and significance of selected biological macromolecules (www.rcsb.org/pdb/molecules/molecule_list.html). Structures highlighted during this past quarter were:

July 2004 -- DNA Ligase: Human cells (with a few unusual exceptions) each contain their own set of 46 long strands of DNA. All of our genetic information is encoded in these strands, with thousands of genes strung along their length. The ordering of genes, and the proximity of one next to the other, can be important for the proper usage of the information, so it is important that our cells protect their DNA from breakage. If one strand in the DNA breaks, it is not a disaster, but it can lead to problems when the DNA double helix is unwound during the processes of transcription and replication. Breakage of both strands, on the other hand, is far more serious. To protect us from these dangers, our cells use DNA ligases to glue together DNA strands that have been broken.

DNA ligase reconnects DNA strands when they are broken. It uses a cofactor molecule for power and a special lysine amino acid to perform the reaction. Our DNA ligases and the DNA ligase from the bacteriophage T7 use ATP as the cofactor. Many bacteria, on the other hand, use NAD in the reaction. In both cases, a lysine in the DNA ligase forms a bond to the phosphate in the cofactor, holding onto the AMP portion and discarding the rest. Later in the reaction, this AMP is transferred to the broken DNA strand, and then is released when the strand is rejoined.

For more information on DNA ligase, see see www.rcsb.org/pdb/molecules/pdb55_1.html.

August 2004 -- Caspases: Billions of cells in your body will die in the next hour. This is entirely normal--the human body continually renews itself, removing obsolete or damaged cells and replacing them with healthy new ones. However, your body must do this carefully. If cells are damaged, like when you cut yourself, they may swell and burst, contaminating the surrounding area. The body responds harshly to this type of cell death, inflaming the area by rushing in blood cells to clean up the mess. To avoid this messy problem, your cells are boobytrapped with a method to die cleanly and quickly on demand. When given the signal, the cell will disassemble its own internal structure and fragment itself into small, tidy pieces that are readily consumed by neighboring cells. This process of controlled, antiseptic death is called apoptosis.

Caspases are the executioners of apoptosis. They are protein-cutting enzymes that chop up strategic proteins in the cell. The name refers to two properties of these enzymes. First, they are cysteine proteases that use the sulfur atom in cysteine to perform the cleavage reaction. Second, they cut proteins next to aspartate amino acids in their chains. They do not cut indiscriminately--instead, they are designed to make exactly the right cuts needed to disassemble the cell in an orderly manner.

For more information on caspases, see www.rcsb.org/pdb/molecules/pdb56_1.html.

September 2004 -- Catalase Living with oxygen is dangerous. We rely on oxygen to power our cells, but oxygen is a reactive molecule that can cause serious problems if not carefully controlled. One of the dangers of oxygen is that it is easily converted into other reactive compounds. Inside our cells, electrons are continually shuttled from site to site by carrier molecules, such as carriers derived from riboflavin and niacin. If oxygen runs into one of these carrier molecules, the electron may be accidentally transferred to it. This converts oxygen into dangerous compounds such as superoxide radicals and hydrogen peroxide, which can attack the delicate sulfur atoms and metal ions in proteins. To make things even worse, free iron ions in the cell occasionally convert hydrogen peroxide into hydroxyl radicals. These deadly molecules attack and mutate DNA. One theory, still controversial, is that this type of oxidative damage accumulates over the years of our life, causing us to age.

Fortunately, cells make a variety of antioxidant enzymes to fight the dangerous side-effects of life with oxygen. Two important players are superoxide dismutase, which converts superoxide radicals into hydrogen peroxide, and catalase, which converts hydrogen peroxide into water and oxygen gas. The importance of these enzymes is demonstrated by their prevalence, ranging from about 0.1% of the protein in an Escherichia coli cell to upwards of a quarter of the protein in susceptible cell types. These many catalase molecules patrol the cell, counteracting the steady production of hydrogen peroxide and keeping it at a safe level.

For more information on catalases, see www.rcsb.org/pdb/molecules/pdb57_1.html.