PDBsum entry 3php

RNA

PDB id: 3php

Contents

DNA/RNA

PDB id:

3php

Name:

RNA

Title:

Structure of the 3' hairpin of the tymv pseudoknot: preformation in RNA folding

Structure:

RNA (5'- r( Gp Gp Up Up Cp Cp Gp Ap Gp Gp Gp Up Cp Ap Up Cp Gp Gp Ap Ap Cp Cp A) -3'). Chain: a. Engineered: yes

Source:

Synthetic: yes. Other_details: RNA was chemically synthesized from turnip yellow mosaic virus

NMR struc:

10 models

Authors:

M.H.Kolk,M.Van Der Graaf,S.S.Wijmenga,C.W.A.Pleij,H.A.Heus, C.W.Hilbers

Key ref:

M.H.Kolk et al. (1998). Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding. Embo J, 17, 7498-7504. PubMed id: 9857204

Date:

13-Oct-98 Release date: 21-Oct-98

DNA/RNA chain

G-G-U-U-C-C-G-A-G-G-G-U-C-A-U-C-G-G-A-A-C-C-A 23 bases

Embo J 17:7498-7504 (1998)

PubMed id: 9857204

Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding.

M.H.Kolk, M.van der Graaf, C.T.Fransen, S.S.Wijmenga, C.W.Pleij, H.A.Heus, C.W.Hilbers.

ABSTRACT

The solution structure of an RNA-hairpin present in the pseudoknot, which is found at the 3'-terminus of turnip yellow mosaic virus genomic RNA, has been solved by nuclear magnetic resonance spectroscopy. The loop, which contains the sequence 5'-GGGUCA-3', was found to be highly structured and, contrary to expectations, does not attain its stability through GA or GC base pair formation but by triple interactions between the tilted adenosine and the minor groove sides of the first two guanosines. Interestingly, a very similar conformation was found for the cognate pseudoknot, implying that the 3'-hairpin is preformed for folding into a pseudoknotted structure. These findings suggest a mechanism of 'predetermined-fit' as a principle in RNA folding.