1QBP

CRYSTAL STRUCTURE OF A BROMINATED RNA HELIX WITH FOUR MISMATCHED BASE PAIRS

Summary for 1QBP

• Entry DOI: 10.2210/pdb1qbp/pdb
• Descriptor: 5'-R(*UP*GP*(CBV)P*(CBV)P*AP*GP*UP*UP*CP*GP*CP*UP*GP*GP*C)-3' (2 entities in total)
• Functional Keywords: brominated cytosine, mismatched base pairs, rna
• Total number of polymer chains: 6
• Total formula weight: 29511.85

Authors

Anderson, A.C.,O'Neil, R.H.,Filman, D.J.,Frederick, C.A. (deposition date: 1999-04-26, release date: 1999-11-26, Last modification date: 2024-02-14)

Primary citation

Anderson, A.C.,O'Neil, R.H.,Filman, D.J.,Frederick, C.A.
Crystal structure of a brominated RNA helix with four mismatched base pairs: An investigation into RNA conformational variability.
Biochemistry, 38:12577-12585, 1999

PubMed Abstract: The X-ray crystal structure of a brominated RNA helix with four mismatched base pairs and sequence r(UG(Br)C(Br)CAGUUCGCUGGC)(2) was determined to 2.1 A using the methods of multiwavelength anomalous diffraction (MAD) applied to the bromine K-absorption edge. There are three molecules in the asymmetric unit with unique crystal-packing environments, revealing true conformational variability at high resolution for this sequence. The structure shows that the sequence itself does not define a consistent pattern of solvent molecules, with the exception of the mismatched base pairs, implying that specific RNA-protein interactions would occur only with the nucleotides. There are a number of significant tertiary interactions, some of which are a result of the brominated base pairs and others that are directly mediated by the RNA 2' hydroxyl groups. The mismatched base pairs exhibit a solvent network as well as a stacking pattern with their nearest neighbors that validate previous thermodynamic analysis.

PubMed: 10504226
DOI: 10.1021/bi9904508

Experimental method

X-RAY DIFFRACTION (2.1 Å)