• RCSB PDB 2004 Annual Report

    This snapshot of the RCSB PDB, which covers the period of July 1, 2003 - June 30, 2004, is intended to provide background information about the resource and describe recent progress and accomplishments. Available online as a PDF (http://www.rcsb.org/pdb/static.do?p=general_information/news_publications/index.html), this report is one of the many RCSB publications designed to keep our user community informed and involved.

  • PDB_EXTRACT and data deposition tools described in Acta D paper

    The options, procedures, and tools for accurate and automated PDB deposition are discussed in a recently published paper. pdb_extract, the PDB Validation Suite, and ADIT are highlighted.

    Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. H. Yang, V. Guranovic, S. Dutta, Z. Feng, H. M. Berman and J. D. Westbrook. Acta Cryst. (2004). D60, 1833-1839 journals.iucr.org/d/issues/2004/10/00/be5021/index.html

  • XML data representation -- PDBML

    A paper discussing the PDB exchange dictionary and the PDB archive files (collectively named "PDBML") has been published online. PDBML files are available from ftp://beta.rcsb.org/pub/pdb/uniformity/data/XML/.

    PDBML: the representation of archival macromolecular structure data in XML. John Westbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick, and Helen M. Berman. Bioinformatics (online October 2004) bioinformatics.oupjournals.org/cgi/content/abstract/bti082

  • PDB Oral History

    RCSB PDB Director Helen M. Berman was interviewed by David Berol (currently a writer for the Eastern Research Group) to discuss the rich history of the Protein Data Bank. Since her beginning days as a crystallographer, Berman believed that protein structure data should be available for archiving and sharing. In this interview, she discusses how the PDB was established at Brookhaven National Laboratory, the impact of community and technology on the archive, and the PDB's transition to the RCSB. Access to this oral history can be arranged through the Chemical Heritage Foundation (www.chemheritage.org/).



  • Cryo-EM Workshop held at RCSB-Rutgers
  • A workshop was held to develop community consensus on the data items needed for deposition of 3D density maps and atomic models derived from cryo-electron microscopy studies. Organized by Helen M. Berman (Rutgers, The State University of New Jersey), Wah Chiu (Baylor College of Medicine), and Michael Rossmann (Purdue University), the Cryo-Microscopy Structure Deposition Workshop was held at RCSB-Rutgers in Piscataway, NJ (October 23-24, 2004). The workshop examined the data items currently collected by EMDep and ADIT for such depositions and discussed desirable additions. Workshop presentations are available from the meeting website at rcsb-dev.rutgers.edu:5015.

    The workshop was sponsored by the RCSB PDB and the Computational Center for Biomolecular Complexes (ncmi.bcm.tmc.edu/ccbc).

  • International Conference on Structural Genomics
  • The RCSB PDB exhibited at the 2004 International Conference on Structural Genomics in Washington, DC (ISGO; November 17-21) and met with the structural genomics community.

  • RCSB PDB Art of Science at Fairleigh Dickinson University
  • In celebration of National Chemistry Week, the RCSB PDB's Art of Science exhibit was at Fairleigh Dickinson University in Teaneck, NJ. Sponsored by the School of Natural Sciences and the Weiner Library of Fairleigh Dickinson University and the Hudson Bergen Chemical Society, an opening reception was held November 19. The exhibit ran until December 19.

  • Database Challenges in Biology Report
  • This report on the September 10, 2004 symposium held at RCSB-CARB by Gary L. Gilliland also appears in the Winter 2004 Newsletter of the American Crystallographic Association.

    Data resources for the biological sciences are acquiring vast amounts of experimentally derived data. The ever-increasing complexity of these data presents challenges to those that develop and manage them. This workshop brought together experts in biological data management who described how they organize these data resources in ways that enable scientists to derive new knowledge about structure and function. The meeting highlighted many of the challenges facing biological database resources that include the increasing rate of data acquisition and complexity, database integration, data validation and data mining. In attendance were nearly 100 scientists from various academic and research institutions, and government agencies.

    After a welcome and brief introduction by Gary Gilliland, (RCSB PDB and CARB), Mark Ellisman (University of California, San Diego) began the presentations with his lecture "Multi-scale Imaging and Databasing of the Nervous System with Advanced Cyberinfrastructure." He focused on data acquisition and analysis issues associated with nervous system data, and provided an overview of several aspects of the Biomedical Informatics Research Network (BIRN, www.nbirn.net/). Next, Wah Chiu (Baylor College of Medicine) lectured on the "Database for Cryo-Electron Microscopy". He described his activities that center around the use of electron crystallography and cryo-electron microscopy to determine the three-dimensional structure of macromolecular assemblies. His presentation included a description of The National Center for Macromolecular Imaging (ncmi.bcm.tmc.edu), an extensive network of collaborative projects, many of which are focused on structural investigation targets that may be critical for use in developing drugs for healthcare. The next presentation by John Johnson (The Scripps Research Institute), "VIrus Particle ExploreR (VIPER): a Database of Standardized Atom Coordinates for Icosahedral Viruses and Derived Description of Subunit Interactions," highlighted the resource at mmtsb.scripps.edu/viper/. The structural data for these structures has been put into a uniform format that allows viewing and analyzing the complete capsid structure.

    In the afternoon, John Markley (University of Wisconsin) presented "Data Management in the Laboratory: User Facilities and Research on Small and Large Scales." The facilities involved include the National Magnetic Resonance Facility (www.nmrfam.wisc.edu/) and BioMagResBank (www.bmrb.wisc.edu). His lecture described the issues associated with the complex data associated with NMR structure determinations, from sample preparation to data analysis, and an approach for capturing these data. Stephen Bryant (National Center for Biotechnology Information; NCBI, www.ncbi.nlm.nih.gov/) then discussed the "Conserved Domain Database: A Protein Family Database." His presentation included a description of novel tools for visualizing and analyzing structural similarities, and illustrated how the structural data is integrated with the functional annotation data and reference information that is generated and maintained by NCBI. Next, Cathy Wu (Georgetown University Medical Center) presented a talk entitled "PIR Integrated Bioinformatics for Functional Genomics and Proteomics." She described the current state of the Protein Information Resource (PIR; pir.georgetown.edu) and how this resource is now involved in UniProt (Universal Protein Resource, www.pir.uniprot.org), a joint effort by PIR, the European Bioinformatics Institute (EBI) and the Swiss Institute of Bioinformatics to consolidate protein sequence information from diverse sources. The final presentation of the day, entitled "The Protein Data Bank: An Integrated Resource for Structural Biology," was given by Helen Berman (Rutgers University and the RCSB PDB). Her talk gave a historical perspective of the PDB, its current status, and future challenges. She capped the day by highlighting many of the issues and advances associated with international efforts to insure a single archive for the structural data. The diversity and challenges of the database activities described by the speakers made this a memorable event.


The Molecule of the Month series, by David S. Goodsell, explores the functions and significance of selected biological macromolecules for a general audience.

October 2004 - G Proteins. Cells communicate by passing small, disposable messages to one another. Some of these messengers travel to distant parts of the body through the blood; others simply diffuse over to a neighboring cell. Then, another cell picks the message up and reads it. Thousands of these messages are used in the human body. Some familiar examples include adrenaline, which controls the level of excitement, glucagon, which carries messages about blood sugar levels, histamine, which signals tissue damage, and dopamine, which relays messages in the nervous system.

In many cases, these molecular messengers never get inside cells. Instead, the message is picked up by a receptor on the cell surface and the signal is then passed from outside to inside through a chain of signaling molecules. G proteins form the central link in this chain of communication. The G protein system is the most common method of signaling in our cells. Thousands of G-protein-coupled receptors have been found on our cells, each waiting for its own particular messenger. Some recognize hormones and make changes in the level of metabolism. Others are used in the nervous system to transmit nerve signals. Our sense of sight also relies on a G protein system that is sensitive to light, and a thousand different forms of these receptors, each recognizing the odor of a different molecule, control our sense of smell. They all share the combination of a receptor that receives a message and a G protein that delivers it inside the cell.

November 2004 - Photosystem II. Photosystem II is the first link in the chain of photosynthesis. It captures photons and uses the energy to extract electrons from water molecules. These electrons are used in several ways. First, when the electrons are removed, the water molecule is broken into oxygen gas, which bubbles away, and hydrogen ions, which are used to power ATP synthesis. This is the source of all of the oxygen that we breathe. Second, the electrons are passed down a chain of electron-carrying proteins, getting an additional boost along the way from photosystem I. As these electrons flow down the chain, they are used to pump hydrogen ions across the membrane, providing even more power for ATP synthesis. Finally, the electrons are placed on a carrier molecule, NADPH, which delivers them to enzymes that build sugar from water and carbon dioxide.

December 2004 - Ubiquitin. As its name implies, ubiquitin is found in all eukaryotic cells and in cells throughout your body. The Nobel Prize in Chemistry was awarded this year to the three researchers who discovered its essential function in 1980. In the subsequent years, it has become apparent that apart from its role in protein disposal, ubiquitin is also used for other tasks, such as directing the transport of proteins in and out of the cell. By connecting ubiquitin together in short or long chains, or using different types of linkages between the molecules, many different signals may be encoded. Because of the important roles it plays, ubiquitin has changed very little over the evolution of life, so you can find a similar form in yeast cells, plant cells, and in our own cells.

The full Molecule of the Month features are available here