PDBsum entry 1a60

RNA

PDB id

1a60

Contents

			DNA/RNA

References listed in PDB file

Key reference

Title

Nmr structure of a classical pseudoknot: interplay of single- And double-Stranded RNA.

Authors

M.H.Kolk, M.Van der graaf, S.S.Wijmenga, C.W.Pleij, H.A.Heus, C.W.Hilbers.

Ref.

Science, 1998, 280, 434-438. [DOI no: 10.1126/science.280.5362.434]

PubMed id

9545221

Abstract

Pseudoknot formation folds the 3' ends of many plant viral genomic RNAs into structures that resemble transfer RNA in global folding and in their reactivity to transfer RNA-specific proteins. The solution structure of the pseudoknotted T arm and acceptor arm of the transfer RNA-like structure of turnip yellow mosaic virus (TYMV) was determined by nuclear magnetic resonance (NMR) spectroscopy. The molecule is stabilized by the hairpin formed by the 5' end of the RNA, and by the intricate interactions related to the loops of the pseudoknot. Loop 1 spans the major groove of the helix with only two of its four nucleotides. Loop 2, which crosses the minor groove, interacts closely with its opposing helix, in particular through hydrogen bonds with a highly conserved adenine. The structure resulting from this interaction between the minor groove and single-stranded RNA at helical junctions displays internal mobility, which may be a general feature of RNA pseudoknots that regulates their interaction with proteins or other RNA molecules.



	Figure 3. Fig. 3. Detail of the structure showing the hydrogen bonds found between loop 2 and stem 1 (see text). The highly DEPC-reactive N-7^ atom of A35 is highlighted in yellow.		Figure 4. Fig. 4. View into the major groove of stem 2 showing the distinct turn in loop 1. The coloring scheme is identical to that of Fig. 2. U24 and U23 are not involved in base-pairing interactions with the opposite bases of A41 and C42. Nucleotides C21 and U22, spanning the major groove, are drawn in thin lines. The curved arrow denotes the direction of the RNA chain.

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