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The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, rcsb.org), the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and Oceania and makes 3D macromolecular structure data available at no charge and without usage restrictions to more than 1 million rcsb.org Users worldwide and 600 000 pdb101.rcsb.org education-focused Users around the globe. PDB Data Depositors include structural biologists using macromolecular crystallography, nuclear magnetic resonance spectroscopy and 3D electron microscopy. PDB Data Consumers include researchers, educators and students studying Fundamental Biology, Biomedicine, Biotechnology and Energy. Recent reorganization of RCSB PDB activities into four integrated, interdependent services is described in detail, together with tools and resources added over the past 2 years to RCSB PDB web portals in support of a ‘Structural View of Biology.’

The tandem zinc finger (TZF) domain of the protein TIS11d binds to the class II AU-rich element (ARE) in the 3' untranslated region (3' UTR) of target mRNAs and promotes their deadenylation and degradation. The NMR structure of the TIS11d TZF domain bound to the RNA sequence 5'-UUAUUUAUU-3' comprises a pair of novel CCCH fingers of type CX(8)CX(5)CX(3)H separated by an 18-residue linker. The two TIS11d zinc fingers bind in a symmetrical fashion to adjacent 5'-UAUU-3' subsites on the single-stranded RNA via a combination of electrostatic and hydrogen-bonding interactions, with intercalative stacking between conserved aromatic side chains and the RNA bases. Sequence specificity in RNA recognition is achieved by a network of intermolecular hydrogen bonds, mostly between TIS11d main-chain functional groups and the Watson-Crick edges of the bases. The TIS11d structure provides insights into the RNA-binding functions of this large family of CCCH zinc finger proteins.

Summary We report the target, biochemical basis, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the α-pyrone antibiotic myxopyronin (Myx). We show that Myx interacts with the RNAP “switch region,” the hinge that mediates opening and closing of the RNAP active-center cleft. We show that Myx prevents interaction of RNAP with promoter DNA. We present a crystal structure that defines contacts between Myx and RNAP and defines effects of Myx on RNAP conformation. We propose that Myx functions by preventing opening of the RNAP active-center cleft to permit entry of DNA during transcription initiation (“hinge jamming”). We establish further that the structurally related α-pyrone antibiotic corallopyronin and the structurally unrelated macrocyclic-lactone antibiotic ripostatin function through the same target and same mechanism. The RNAP switch region is an attractive target for identification of new broad-spectrum antibacterial therapeutic agents.

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