5V2R

Structure of a GA Rich 8x8 Nucleotide RNA Internal Loop

Summary for 5V2R

• Entry DOI: 10.2210/pdb5v2r/pdb
• NMR Information: BMRB: 30268
• Descriptor: RNA (5'-R(*CP*CP*AP*GP*AP*AP*AP*CP*GP*GP*AP*UP*GP*GP*A)-3') (1 entity in total)
• Functional Keywords: 3rrs ga sheared pairs ac pair, rna
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 9756.04

Authors

Kauffmann, A.D.,Kennedy, S.D.,Turner, D.H. (deposition date: 2017-03-06, release date: 2017-07-26, Last modification date: 2024-05-01)

Primary citation

Kauffmann, A.D.,Kennedy, S.D.,Zhao, J.,Turner, D.H.
Nuclear Magnetic Resonance Structure of an 8 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions.
Biochemistry, 56:3733-3744, 2017

PubMed Abstract: The prediction of RNA three-dimensional structure from sequence alone has been a long-standing goal. High-resolution, experimentally determined structures of simple noncanonical pairings and motifs are critical to the development of prediction programs. Here, we present the nuclear magnetic resonance structure of the (5'CCAGAAACGGAUGGA) duplex, which contains an 8 × 8 nucleotide internal loop flanked by three Watson-Crick pairs on each side. The loop is comprised of a central 5'AC/3'CA nearest neighbor flanked by two 3RRs motifs, a known stable motif consisting of three consecutive sheared GA pairs. Hydrogen bonding patterns between base pairs in the loop, the all-atom root-mean-square deviation for the loop, and the deformation index were used to compare the structure to automated predictions by MC-sym, RNA FARFAR, and RNAComposer.

PubMed: 28700212
DOI: 10.1021/acs.biochem.7b00201

Experimental method

SOLUTION NMR