405d

STRUCTURE OF A 16-MER RNA DUPLEX R(GCAGACUUAAAUCUGC)2 WITH WOBBLE LIKE A.C MISMATCHES

spinqualitylabelsall models 405d, resolution 2.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 405d is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed The crystal structure of a 16-mer, the longest known RNA duplex, has been determined at 2.5 A resolution. The hexadecamer r(GCAGACUUAAAUCUGC) contains isolated C.A/A.C mismatches with two hydrogen bonds. The two hydrogen bonds in the mismatches suggests that N1 of A is protonated even though the crystallization was done at neutral pH. Therefore, the C.A mismatch is a C.A+ wobble similar to the G.U wobble. The two C.A+ pairs are isolated by four Watson-Crick pairs and flanked by five Watson-Crick base-pairs on either sides. Kinks/bends of 20 degrees are observed at the wobble sites. The Watson-Crick base-pair A5.U26 on the 5'-side of the first C6.A27(+) wobble has a twist angle of 27 degrees compared to the 3'-side U7.A28 pair of 36 degrees. The twist angles are reversed (37 degrees and 26 degrees) in the second A11(+).C22 wobble because of the approximate dyad in the molecule, the flanking base-pair sequences are A.U pairs. The wobbles expand the major groove to 7.1 A/7.3 A. The duplexes form helical columns and are tightly packed around the 31-screw axis. The minor grooves of adjacent columns in juxtaposition interact through the O2' atoms and the anionic phosphate oxygen atoms.Copyright 1998 Academic Press. Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches.,Pan B, Mitra SN, Sundaralingam M J Mol Biol. 1998 Nov 13;283(5):977-84. PMID:9799637 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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