The crystal structure of the RNA dodecamer 5'-GGACUUUGGUCC-3' has been determined from X-ray diffraction data to 2.6 A resolution. This oligomer forms an asymmetric double helix in the crystal. Four consecutive non-Watson-Crick base-pairs are formed in the middle of the duplex including the first intrahelical U-U (or T-T) pairs observed in an oligonucleotide crystal structure. Two different conformations of U-U pairs are observed in the context of the surrounding sequence. One of these pairs is highly twisted, allowing a bound water to bridge across strands in the major groove. The crystal packing illustrates a new form of RNA helix-helix interaction.
The crystal structure of the RNA dodecamer 5-GGCC(GAAA)GGCC-3 has been determined from x-ray diffraction data to 2.3-Å resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G⅐A pairs and novel asymmetric A⅐A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34؇ from end to end and the diameter is narrowed by 24% in the internal loop. A Mn 2؉ ion is bound directly to the N7 of the first guanine in the Watson-Crick region following the internal loop and the phosphate of the preceding residue. This Mn 2؉ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.The study of RNA structure by NMR and x-ray crystallographic methods is currently flourishing due to both improvements in methods of synthesis and purification and the impetus provided by discoveries of new biological functions of RNA. A common element of RNA secondary structure is the internal loop, an interruption in double helical RNA by a series of bases that cannot form standard Watson-Crick pairs. Internal loops are found, for example, in ribosomal RNA, ribozymes, viroids, protein regulatory sites, and SELEX-evolved RNAs. Characterization of the three-dimensional structure of internal loops and their effect on the helices that bracket them is still in an early stage. The crystal structures of several RNA oligomers incorporating symmetric internal loops have been previously determined (1-4) and shown to have continuous base pairing with formation of U⅐G, U⅐C, and U⅐U non-Watson-Crick pairs. The helices containing these internal loops generally retain an A-form geometry; however, the presence of tandem U⅐C base pairs in one structure (1) induced a dramatic widening of the major groove from about 4 Å to about 8 Å. Perturbations in regular RNA helices by internal loops may be utilized by regulatory proteins to recognize specific RNA structures such as the rev-responsive element (RRE) (5) and the iron regulatory element (IRE) (6). Recently, it has been shown that the G⅐U mispair responsible for recognition and aminoacylation of tRNA Ala by its synthetase can be substituted by other non-Watson-Crick base pairs, implying that distortion in the helix induced by mispairing and not a particular sequence may be responsible for recognition (7).
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The 1.4 A resolution structure of recombinant mouse tumour-necrosis factor alpha (mTNF) at 100 K has been determined. The crystals are triclinic, space group P1, with unit-cell parameters a = 48.06, b = 48.18, c = 51.01 A, alpha = 114.8, beta = 103.6, gamma = 91.1 degrees. The structure was refined to a final crystallographic R value of 19.7% (Rfree = 23.3%), including 3477 protein atoms, one 2-propanol molecule, one Tris molecule and 240 water molecules. Throughout the crystal lattice, the trimers are differently packed compared with human TNF, which was crystallized in the tetragonal space group P41212 and refined to 2.6 A resolution. The structures of mTNF and human TNF are very similar, diverging mainly in regions that are either flexible and/or involved in crystal packing. Some loops in mTNF which contain residues important for receptor binding are better resolved than in human TNF, such as the surface-exposed loops 30-34 and 144-147, which are also important for receptor specificity. Compared with human TNFs, the channel formed by the three monomers in mTNF is narrower. One 2-propanol molecule trapped in the trimeric channel could be a lead compound for the design of TNF inhibitors.
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