The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235-242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.

The specificity of vesicular transport is regulated, in part, by the interaction of a vesicle-associated membrane protein termed synaptobrevin/VAMP with a target compartment membrane protein termed syntaxin. These proteins, together with SNAP-25 (synaptosomeassociated protein of 25 kDa), form a complex which serves as a binding site for the general membrane fusion machinery. Synaptobrevin/VAMP and syntaxin are ubiquitously expressed proteins and are believed to be involved in vesicular transport in most (if not all) cells. However, SNAP-25 is present almost exclusively in the brain, suggesting that a ubiquitously expressed homolog of SNAP-25 exists to facilitate transport vesicle/target membrane fusion in other tissues. Using the yeast two-hybrid system, we have identified a 23-kDa protein from human B lymphocytes (termed SNAP-23) that binds tightly to multiple syntaxins and synaptobrevins/ VAMPs in vitro. SNAP-23 is 59% identical with SNAP-25. Unlike SNAP-25, SNAP-23 was expressed in all tissues examined. These findings suggest that SNAP-23 is an essential component of the high affinity receptor for the general membrane fusion machinery and an important regulator of transport vesicle docking and fusion in all mammalian cells.A fundamental goal of cell biology is the elucidation of the molecular steps involved in intracellular protein transport. In general, this process involves the liberation of cargo-containing transport vesicles from "donor" membranes and the subsequent docking and fusion of these vesicles with target, or "acceptor" membranes (1). It is clear that vesicle docking and vesicle fusion are distinct processes mediated by distinct proteins (reviewed in Refs. 2 and 3). Since the general membrane fusion machinery (consisting of NSF 1 and SNAPs) nonspecifically catalyzes membrane fusion, the regulation of fusion between transport vesicles and specific acceptor membranes is thought to lie in the vesicle docking process. In the brain, synaptic vesicle docking is regulated in part by specific interactions of the synaptic vesicle protein synaptobrevin (also known as vesicle-associated membrane protein or VAMP) with the presynaptic plasma membrane-associated proteins syntaxin and SNAP-25 (synaptosome-associated protein of 25 kDa; not related to the SNAPs for NSF). Together these molecules form a stable complex which also functions as a SNAP receptor ("SNARE"). It is believed SNAPs and NSF bind to the SNARE complex at the transport vesicle/target membrane interface so that following vesicle docking membrane fusion can occur.A general model of protein transport in all cells, the SNARE hypothesis, proposes that the specificity of a particular transport step is regulated by the specific interaction of distinct VAMPs and syntaxins on transport vesicles and target (acceptor) membranes, respectively (4). There is considerable experimental evidence to support the SNARE hypothesis, including the demonstration that (a) different isoforms of syntaxin and VAMP exist, some of which can be localized to unique intracellu...

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

The cytoskeletal changes that alter cellular morphogenesis and motility depend upon a complex interplay among molecules that regulate actin, myosin, and other cytoskeletal components. The Rho family of GTP binding proteins are important upstream mediators of cytoskeletal organization. Gem and Rad are members of another family of small GTP binding proteins (the Rad, Gem, and Kir family) for which biochemical functions have been mostly unknown. Here we show that Gem and Rad interface with the Rho pathway through association with the Rho effectors, Rho kinase (ROK) α and β. Gem binds ROKβ independently of RhoA in the ROKβ coiled-coil region adjacent to the Rho binding domain. Expression of Gem inhibited ROKβ-mediated phosphorylation of myosin light chain and myosin phosphatase, but not LIM kinase, suggesting that Gem acts by modifying the substrate specificity of ROKβ. Gem or Rad expression led to cell flattening and neurite extension in N1E-115 neuroblastoma cells. In interference assays, Gem opposed ROKβ- and Rad opposed ROKα-mediated cell rounding and neurite retraction. Gem did not oppose cell rounding initiated by ROKβ containing a deletion of the Gem binding region, demonstrating that Gem binding to ROKβ is required for the effects observed. In epithelial or fibroblastic cells, Gem or Rad expression resulted in stress fiber and focal adhesion disassembly. In addition, Gem reverted the anchorage-independent growth and invasiveness of Dbl-transformed fibroblasts. These results identify physiological roles for Gem and Rad in cytoskeletal regulation mediated by ROK.