1RRR

RNA DUPLEX CONTAINING A PURINE-RICH STRAND, NMR, 10 STRUCTURES

1RRR の概要

• エントリーDOI: 10.2210/pdb1rrr/pdb
• 分子名称: RNA (5'-R(*GP*AP*AP*GP*AP*GP*AP*AP*GP*C)-3'), RNA (5'-R(*GP*CP*UP*UP*CP*UP*CP*UP*UP*C)-3') (2 entities in total)
• 機能のキーワード: rna duplex, purine/pyrimidine-rich strands, a-form, rna
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6338.88

構造登録者

Gyi, J.I.,Lane, A.N.,Conn, G.L.,Brown, T. (登録日: 1997-10-21, 公開日: 1998-04-22, 最終更新日: 2024-05-22)

主引用文献

Gyi, J.I.,Lane, A.N.,Conn, G.L.,Brown, T.
Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes.
Biochemistry, 37:73-, 1998

PubMed Abstract: The structures of d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC). r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), and r(GAAGAGAAGC). r(GCUUCUCUUC) have been determined in solution from NMR data. Globally, the pure DNA and RNA duplexes were in the B and A forms, respectively. The two DNA.RNA hybrids were neither A nor B, but closer globally to the A than the B form. However, the thermodynamically less stable d(GAAGAGAAGC).r(GCUUCUCUUC) duplex has a significantly different conformation from r(GAAGAGAAGC). d(GCTTCTCTTC). Structures were calculated based on the NMR data, using restrained molecular dynamics. A new approach to the treatment of conformational averaging based on a prioriprobabilities has been used. The nucleotides were treated by fitting the scalar coupling data and NOE time courses to a two-state model comprising N and S sugar puckers each with a different glycosidic torsion angle, and the mole fraction of the S state. Restraint sets for different distributions of N and S states within molecules were constructed, such that each nucleotide was weighted in the ensemble according to the mole fractions (or a prioriprobabilities). The individual nucleotide conformations were strongly restrained, whereas the internucleotide restraints were set relatively loosely. Ensembles of conformations were generated and assessed by comparison of the NOEs calculated from ensemble-averaged relaxation matrices with the experimental NOEs. The ensemble averages accounted for the experimental data much better than any individual member, or for structures calculated assuming a single unique conformation. The two hybrids populated different degrees of conformational space. There was a general trend in minor and major groove widths in the order d(GAAGAGAAGC).d(GCTTCTCTTC), d(GAAGAGAAGC).r(GCUUCUCUUC), r(GAAGAGAAGC).d(GCTTCTCTTC), r(GAAGAGAAGC).r(GCUUCUCUUC) and a similar progression in global character from B-like to A-like structures. Furthermore, r(GAAGAGAAGC).d(GCTTCTCTTC) showed a greater dispersion of conformations in the ensemble than d(GAAGAGAAGC).r(GCUUCUCUUC), reflecting the greater flexibility of the sugars. If conformational averaging of the nucleotides is ignored, incorrect virtual structures are produced that nevertheless are able to satisfy a substantial fraction of the experimental data.

PubMed: 9425027
DOI: 10.1021/bi9719713

実験手法

SOLUTION NMR