1mfj
From Proteopedia
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3' Stem-Loop from Human U4 SNRNA
Overview
The NMR structure of the 3' stem-loop (3'SL) from human U4 snRNA was, determined to gain insight into the structural basis for conservation of, this stem-loop sequence from vertebrates. 3'SL sequences from human, rat, mouse and chicken U4 snRNA each consist of a 7 bp stem capped by a UACG, tetraloop. No high resolution structure has previously been reported for a, UACG tetraloop. The UACG tetraloop portion of the 3'SL was especially well, defined by the NMR data, with a total of 92 NOE-derived restraints (about, 15 per residue), including 48 inter-residue restraints (about 8 per, residue) for the tetraloop and closing C-G base pair. Distance restraints, were derived from NOESY spectra using MARDIGRAS with random error, analysis. Refinement of the 20mer RNA hairpin structure was carried out, using the programs DYANA and miniCarlo. In the UACG tetraloop, U and G, formed a base pair stabilized by two hydrogen bonds, one between the, 2'-hydroxyl proton of U and carbonyl oxygen of G, another between the, imino proton of G and carbonyl oxygen O2 of U. In addition, the amino, group of C formed a hydrogen bond with the phosphate oxygen of A. G, adopted a syn orientation about the glycosidic bond, while the sugar, puckers of A and C were either C2'-endo or flexible. The conformation of, the UACG tetraloop was, overall, similar to that previously reported for, UUCG tetraloops, another member of the UNCG class of tetraloops. The, presence of an A, rather than a U, at the variable position, however, presents a distinct surface for interaction of the 3'SL tetraloop with, either RNA or protein residues that may stabilize interactions important, for active spliceosome formation. Such tertiary interactions may explain, the conservation of the UACG tetraloop motif in 3'SL sequences from U4, snRNA in vertebrates.
About this Structure
1MFJ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of the 3' stem-loop from human U4 snRNA., Comolli LR, Ulyanov NB, Soto AM, Marky LA, James TL, Gmeiner WH, Nucleic Acids Res. 2002 Oct 15;30(20):4371-9. PMID:12384583
Page seeded by OCA on Sun Nov 25 04:10:11 2007
