Electron Microscopy Data Bank

PACS PCA PDB PEEM PESTM PET PrP Picture Archiving and Communication Systems Principal Component Analysis Protein Data Bank Photoemission Electron Microscopy STM Photoemission Spectroscopy Positron Emission Tomography Prion Protein... 

X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and electron microscopy are widely used to determine the structures of proteins and their complexes. These structures have been deposited in Protein Data Bank (PDB) and are available at http /Avww.rcsb.org/ (1). Currently, the PDB has nearly 50,000 structures, and the wealth of data provide valuable information on relating the structures of proteins with their functions, interactions, and evolution. For example, the structure of a protein explicitly reveals the presence of various interactions, cavities, clefts, active sites, binding regions, and so forth. 

The Protein Data Bank (PDB) was established as a service to international science at the Brookhaven National Laboratory in the United States in 1971 to store and curate the atomic coordinates of macromo-lecular stmctures. Original versions of the whole data bank were distributed on magnetic tape to scientists, then on compact discs, and now they are freely available via the Internet (http //www.rcsb.org/). The PDB is part of the wwPDB whose mission is to ensure that the PDB archive remains an international resource with uniformly coded data. Other related sites are located in Japan (PDBj, http //www.pdbj.org/) and in Europe (MSD-EBI, http //www.ebi.ac.uk/msd/). In addition to coordinates, the PDB stores experimental diffraction data, and it provides many tools for analyzing and displaying structures. As of April 15, 2008, the PDB held 50,277 sets of atomic coordinates from proteins, nucleic acids, and carbohydrates determined by X-ray diffraction, NMR spectroscopy, and electron microscopy. About 5000 new stmctures are released each year, and the database is expected to treble to 150,000 by 2014. 

The structures of proteins are the key data for understanding the functions of proteins. There are three main techniques for measuring the structures of proteins nuclear magnetic resonance (NMR), cryo-electron microscopy (cryo-EM) and protein crystallography (X-ray diffraction). The solved structures of macromolecules, including proteins, nucleic acids and their complexes, are deposited in the Protein Data Bank (PDB). Up to 23 June of 2009, a total of 58 414 structures of macromolecules had been released in the PDB, and these were mostly protein structures (Table 7.1). Among these structures, about 86% were determined by protein crystallography. 

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