1A60

NMR STRUCTURE OF A CLASSICAL PSEUDOKNOT: INTERPLAY OF SINGLE-AND DOUBLE-STRANDED RNA, 24 STRUCTURES

Summary for 1A60

• Entry DOI: 10.2210/pdb1a60/pdb
• NMR Information: BMRB: 4120
• Descriptor: TYMV PSEUDOKNOT (1 entity in total)
• Functional Keywords: rna, pseudoknot, tymv, ribonucleic acid
• Biological source: Turnip yellow mosaic virus
• Total number of polymer chains: 1
• Total formula weight: 13984.33

Authors

Kolk, M.H.,Van Der Graaf, M.,Wijmenga, S.S.,Pleij, C.W.A.,Heus, H.A.,Hilbers, C.W. (deposition date: 1998-03-04, release date: 1998-05-27, Last modification date: 2024-05-22)

Primary citation

Kolk, M.H.,van der Graaf, M.,Wijmenga, S.S.,Pleij, C.W.,Heus, H.A.,Hilbers, C.W.
NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA.
Science, 280:434-438, 1998

PubMed 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.

PubMed: 9545221
DOI: 10.1126/science.280.5362.434

Experimental method

SOLUTION NMR