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Table of Contents RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS Rutgers, The State University of New Jersey University of California, San Diego Table of Contents About the Cover The front cover maps the proteins and chemical reactions involved with the metabolic pathway called the citric Message from the Director ......................................3 acid cycle . Also known as the Krebs cycle or the tricarboxylic acid The RCSB PDB and the PDB Archive ...................4 cycle, the citric acid cycle is at the center of cellular me - tabolism. It plays a starring role in both the process of energy production and biosynthesis. The cycle finishes the sugar-breaking job started in glycolysis and fuels the PDB Structures ............................................................5 production of ATP in the process. It is also a central hub in biosynthetic reactions, providing intermediates that are used to build amino acids and other molecules. Cit - Data Deposition, Processing, and Annotation .......6 ric acid cycle enzymes are found in all cells that use oxy - gen, and even in some cells that don't. The eight reactions of the citric acid cycle use a small Related wwPDB Initiatives ......................................8 molecule –oxaloacetate –as a catalyst. The cycle starts by addition of an acetyl group to oxaloacetate, then, in eight steps, the acetyl group is completely broken apart, Data Access, Query, and Reporting ....................10 restoring the oxaloacetate molecule for another round. In a typically biological twist, it's not quite this simple. You might imagine that the enzymes could just pop off PDB-101, Outreach, and Education ...................14 the two carbon atoms of the acetyl group, using the oxaloacetate as a convenient carrier. However, by care - fully labeling particular carbon atoms in these mole - cules, scientists have found that things get shuffled Related Resources ...................................................18 around a bit, and two carbon atoms in the original oxaloacetate are the parts that are actually released as carbon dioxide. Then, at the end of the cycle, the original References and Acknowledgements ................18 acetate atoms are shuffled around to recreate the oxaloacetate. The structures shown here, taken from several different organisms, are explored further in the October 2012 Mole - cule of the Month (doi:10.2210/rcsb_pdb/mom_2012_10 ). Illustration created with guidance from Fundamentals of Biochemistry. 63 Citric Acid Cycle Enzymes The metabolite atoms on the front cover are depicted as follows: Oxygen Carbon Hydrogen Sulfur malate dehydrogenase (1mld) 75 citrate synthase (1cts) 64 fumarase (1fuo) 74 aconitase (7acn) 65 succinate dehydrogenase (1nek) 73 isocitrate dehydrogenase (3blw) 66 succinyl-CoA 72 synthetase (2fp4) 2-oxoglutarate dehydrogenase complex (1e2o, 67 1bbl, 68 1pmr, 69 2eq7, 70 and 2jgd) 71 Message from the Director 3 With the goal of enabling a structural view of biology, the RCSB PDB organ - ization takes on many roles. At its core is the Protein Data Bank (PDB) archive, a key repository of information describing proteins, nucleic acids, and other important biological macromolecular machines that help inform our understanding of biology and medicine. Along with our Worldwide PDB collaborators, the RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers. This information is then streamlined for students and teachers in the form of the educational site called PDB-101. This annual report gives a glimpse of the RCSB PDB activities that help drive these efforts. During the reporting period of July 1, 2011 - June 30, 2012, the RCSB PDB has reached several milestones while simultaneously preparing for an exciting future. In March 2012, 80,000 entries became available in the archive. The PDB reached the 70,000 mark in December 2010. Other PDB numbers: 9250 entries were deposited and annotated in the calendar year 2011, and 8076 were released into the archive (compared with 8878 depositions and 7897 released entries in the previous year). Data were downloaded 379 million times in 2011, compared with 209 million in 2010. Other milestones have been reached near and far. Of local note, team members at Rutgers are happy to report that they have settled into the Center for Integrative Proteomics Research building. This new facility was built to join together structural biology, bioinformatics, and proteomics research groups on campus. These include the RCSB PDB, core facilities, research laboratories, and meeting space. This building has already hosted several meetings and workshops, including the Worldwide PDB’s Small Angle Scattering Task Force. Globally, the wwPDB continues to collaborate on several projects that will take the PDB into the next generation. As the amount of data deposited to the PDB increases, the need to develop more streamlined methods for processing and validation becomes greater. To this end, the wwPDB has made significant progress on the development of a Common Deposition and Annotation tool that will be used by all wwPDB sites to more effectively capture and process PDB depositions. External testing will begin in 2013. The versatile, knowledgeable, and creative team of scientists, developers, and educators at the RCSB PDB look forward to reaching even more milestones in the coming year. Helen M. Berman Director, RCSB PDB Board of Governors Professor of Chemistry and Chemical Biology Center for Integrative Proteomics Research in Piscataway, NJ Rutgers, The State University of New Jersey The RCSB PDB and the PDB Archive 4 Funding The RCSB PDB: Enabling Science and Education Worldwide The RCSB PDB is supported by funds from the: The RCSB Protein Data Bank 1 provides a global resource for the advancement of research and education in biology and medicine by • National Science curating, integrating, and disseminating biological macromolecular Foundation structural information in the context of function, biological processes, (NSF DBI 0829586) evolution, pathways, and disease states. • National Institute of General NIGMS Administered by the Research Collaboratory for Structural Bioinfor - Medical Sciences (NIGMS) matics (RCSB), the RCSB PDB builds upon the data available in the • Office of Science, PDB archive by creating tools and educational materials for use by Department of Energy (DOE) researchers, teachers, and students studying a variety of fields focused • National Library of Medicine on biology: molecular biology, structural biology, computational (NLM) biology, pharmacology, and others. • National Cancer Institute Through its online resources and interactions with its user commu - (NCI) nities, the RCSB PDB helps to answer broad biological questions • National Institute of where macromolecular structure is key. Neurological Disorders and Stroke (NINDS) PDB: A Community Resource for Science • National Institute of In the late 1950s, scientists began to decipher the 3D shapes of proteins Diabetes & Digestive & at an atomic level. As structures were determined using X-ray crystallog - Kidney Diseases (NIDDK) raphy, early computer graphics programs provided interactive views of these macromolecules. The possibilities for science and knowledge seen in these glimpses of myoglobin, 2,3 hemoglobin, 4,5 lysozyme, 6,7 and ribonuclease 8,9 inspired a new field of structural biology. The potential research that could be enabled by archiving and sharing data from these experiments moved the scientific community to action. was part of the team that first envisioned the PDB archive. Dr. Martha Beginning with only seven structures, the PDB archive was es tablished Quesada, Deputy Director (Rutgers), and Professor Philip E. Bourne, in 1971 to provide both a home and access point for the data produced Associate Director (UCSD), join her in RCSB PDB management. from these experiments. 10 Scientists would send their coordinate data to the PDB, who would then mail them to interested users. The RCSB PDB Team is composed of experts in diverse fields of computer science, biology, chemistry, and education. In addition to working Today, the PDB contains and supports online access to more than with PDB data, RCSB PDB members co-author scientific papers, 80,000 biomacromolecules that help researchers understand all aspects exhibit at meetings, present posters and papers, and attend and of biomedicine and agriculture, from protein synthesis to health and organize workshops. Staff members also serve as tutors, teachers, and disease to biological energy. Data are deposited by scientists from mentors to students of all ages. around the world, and used by a growing number of researchers in a variety of fields. The RCSB PDB receives input from an advisory board of experts in X-ray crystallography, nuclear magnetic resonance (NMR), 3D electron The PDB archive is managed by the World - microscopy (3DEM), bioinformatics, and education. wide Protein Data Bank (wwPDB), 11 a con - sortium of groups that host deposition, annotation, and distribution centers for PDB data and collaborate on a variety of projects and outreach efforts. Each wwPDB member develops separate websites, tools, and resources to access and analyze PDB data. As a member, the RCSB PDB collab - orates with the wwPDB on matters relating to getting data in the archive, while independently developing tools
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