PDBsum entry 1k8s

RNA

PDB id: 1k8s

Contents

DNA/RNA

PDB id:

1k8s

Name:

RNA

Title:

Bulged adenosine in an RNA duplex

Structure:

5'-r( Gp Gp Cp Ap Gp Ap Gp Up Gp Cp Cp Gp C)-3'. Chain: a. Engineered: yes. Other_details: bulged base RNA duplex e coli 5s rrna. 5'-r( Gp Cp Gp Gp Cp Ap Cp Cp Up Gp Cp C)-3'. Chain: b. Engineered: yes

Source:

Synthetic: yes. Other_details: enzymatically synthesized using t7 RNA polymerase.. Other_details: enzymatically synthesized using t7 RNA polymerase.

NMR struc:

1 models

Authors:

V.Thiviyanathan,A.B.Guliaev,N.B.Leontis,D.G.Gorenstein

Key ref:

V.Thiviyanathan et al. (2000). Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement. J Mol Biol, 300, 1143-1154. PubMed id: 10903860 DOI: 10.1006/jmbi.2000.3931

Date:

25-Oct-01 Release date: 14-Nov-01

DNA/RNA chains

G-G-C-A-G-A-G-U-G-C-C-G-C 13 bases

G-C-G-G-C-A-C-C-U-G-C-C 12 bases

DOI no: 10.1006/jmbi.2000.3931

J Mol Biol 300:1143-1154 (2000)

PubMed id: 10903860

Solution conformation of a bulged adenosine base in an RNA duplex by relaxation matrix refinement.

V.Thiviyanathan, A.B.Guliaev, N.B.Leontis, D.G.Gorenstein.

ABSTRACT

Bulges are common structural motifs in RNA secondary structure and are thought to play important roles in RNA-protein and RNA-drug interactions. Adenosine bases are the most commonly occurring unpaired base in double helical RNA secondary structures. The solution conformation and dynamics of a 25-nucleotide RNA duplex containing an unpaired adenosine, r(GGCAGAGUGCCGC): r(GCGGCACCUGCC) have been studied by NMR spectroscopy and MORASS iterative relaxation matrix structural refinement. The results show that the bulged adenosine residue stacks into the RNA duplex with little perturbation around the bulged region. Most of the bases in the RNA duplex adopt C(3)'-endo conformation, exhibiting the N-type sugar pucker as found in the A form helices. The sugars of the bulged residue and the 5' flanking residue to it are found to exhibit C(2)'-endo conformation. None of the residues are in syn conformation.

Selected figure(s)

Figure 1.
Figure 1. Sequence of the RNA duplex with the bulged adenosine.

Figure 6.
Figure 6. Overlay of the final averaged structures from r-MD with and without backbone dihedral restraints.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 300, 1143-1154) copyright 2000.

Figures were selected by the author.