1ATO

THE STRUCTURE OF THE ISOLATED, CENTRAL HAIRPIN OF THE HDV ANTIGENOMIC RIBOZYME, NMR, 10 STRUCTURES

Summary for 1ATO

• Entry DOI: 10.2210/pdb1ato/pdb
• Descriptor: RNA (5'-R(*GP*GP*CP*AP*CP*CP*UP*CP*CP*UP*CP*GP*CP*GP*GP*UP*GP*CP*C)-3') (1 entity in total)
• Functional Keywords: central loop, hepatitis delta virus, ribozyme, rna hairpin, rna
• Biological source: Hepatitis delta virus
• Total number of polymer chains: 1
• Total formula weight: 6020.62

Authors

Kolk, M.H.,Heus, H.A.,Hilbers, C.W. (deposition date: 1997-08-14, release date: 1997-11-12, Last modification date: 2024-05-22)

Primary citation

Kolk, M.H.,Heus, H.A.,Hilbers, C.W.
The structure of the isolated, central hairpin of the HDV antigenomic ribozyme: novel structural features and similarity of the loop in the ribozyme and free in solution.
EMBO J., 16:3685-3692, 1997

PubMed Abstract: The structure of an RNA hairpin containing a seven-nucleotide loop that is present in the self-cleaving sequence of hepatitis delta virus antigenomic RNA was determined by high resolution NMR spectroscopy. The loop, which is composed of only one purine and six pyrimidines, has a suprisingly stable structure, mainly supported by sugar hydroxyl hydrogen bonds and base-base and base-phosphate stacking interactions. Compared with the structurally well-determined, seven-membered anticodon loop in tRNA, the sharp turn which affects the required 180 degrees change in direction of the sugar-phosphate backbone in the loop is shifted one nucleotide in the 3' direction. This change in direction can be characterized as a reversed U-turn. It is expected that the reversed U-turn may be found frequently in other molecules as well. There is evidence for a new non-Watson-Crick UC base pair formed between the first and the last residue in the loop, while most of the other bases in the loop are pointing outwards making them accessible to solvent. From chemical modification, mutational and photocrosslinking studies, a similar picture develops for the structure of the hairpin in the active ribozyme indicating that the loop structure in the isolated hairpin and in the ribozyme is very similar.

PubMed: 9218809
DOI: 10.1093/emboj/16.12.3685

Experimental method

SOLUTION NMR