165D

THE STRUCTURE OF A MISPAIRED RNA DOUBLE HELIX AT 1.6 ANGSTROMS RESOLUTION AND IMPLICATIONS FOR THE PREDICTION OF RNA SECONDARY STRUCTURE

Summary for 165D

• Entry DOI: 10.2210/pdb165d/pdb
• Descriptor: DNA/RNA (5'-R(*GP*CP*UP*UP*CP*GP*GP*CP*)-D(*(BRU))-3'), RHODIUM HEXAMINE ION (3 entities in total)
• Functional Keywords: a-dna/rna, double helix, overhanging bases, modified, mismatched, dna-rna hybrid
• Total number of polymer chains: 2
• Total formula weight: 6595.56

Authors

Cruse, W.,Saludjian, P.,Biala, E.,Strazewski, P.,Prange, T.,Kennard, O. (deposition date: 1994-03-21, release date: 1994-08-31, Last modification date: 2024-02-07)

Primary citation

Cruse, W.B.,Saludjian, P.,Biala, E.,Strazewski, P.,Prange, T.,Kennard, O.
Structure of a mispaired RNA double helix at 1.6-A resolution and implications for the prediction of RNA secondary structure.
Proc.Natl.Acad.Sci.USA, 91:4160-4164, 1994

PubMed Abstract: The nonamer r(GCUUCGGC)dBrU, where dBrU is 5-bromo-2'-deoxyuridine, contains the tetraloop sequence UUCG. It crystallizes in the presence of Rh(NH3)6Cl3. In solution the oligomer is expected to form a hairpin loop but the x-ray structure analysis, to a resolution of 1.6 A, indicates an eight-base-pair A-RNA duplex containing a central block of two G.U and two C.U pairs. Self-pairs which approximate to Watson-Crick geometry are also formed in the extended crystal structure between symmetry-related BrU residues and are part of infinite double-helical stacks. The G.U pair is a wobble base pair analogous to the G.T pair found in DNA fragments. The C.U mismatch involves one hydrogen-bonded contact between the bases and a bridging water molecule which ensures a good fit of the base pair in the RNA helix. The BrU.BrU pair is held by two hydrogen bonds in an orientation which is compatible with duplex geometry. The structure observed within the crystal has some parallels with the structure of globular RNAs, and the presence of stable, noncanonical base pairs has implications for the prediction of RNA secondary structure.

PubMed: 7514296
DOI: 10.1073/pnas.91.10.4160

Experimental method

X-RAY DIFFRACTION (1.55 Å)