405D

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

Summary for 405D

• Entry DOI: 10.2210/pdb405d/pdb
• Descriptor: RNA (5'-R(*GP*CP*AP*GP*AP*CP*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3') (2 entities in total)
• Functional Keywords: a-rna double helix, rna
• Total number of polymer chains: 2
• Total formula weight: 10164.16

Authors

Pan, B.,Sundaralingam, M.,Mitra, S.N. (deposition date: 1998-06-17, release date: 1999-01-13, Last modification date: 2024-02-28)

Primary citation

Pan, B.,Mitra, S.N.,Sundaralingam, M.
Structure of a 16-mer RNA duplex r(GCAGACUUAAAUCUGC)2 with wobble C.A+ mismatches.
J.Mol.Biol., 283:977-984, 1998

PubMed Abstract: 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.

PubMed: 9799637
DOI: 10.1006/jmbi.1998.2140

Experimental method

X-RAY DIFFRACTION (2.5 Å)