422D

5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3'

Summary for 422D

• Entry DOI: 10.2210/pdb422d/pdb
• Descriptor: 5'-R(*GP*AP*UP*CP*AP*CP*UP*UP*CP*GP*GP*U)-3' (2 entities in total)
• Functional Keywords: double helix, rna
• Total number of polymer chains: 2
• Total formula weight: 7578.56

Authors

Eswaramoorthy, S.,Rao, S.T.,Sundaralingam, M. (deposition date: 1998-09-10, release date: 2003-06-03, Last modification date: 2024-04-03)

Primary citation

Eswaramoorthy, S.,Rao, S.T.,Pan, B.,Sundaralingam, M.
Structure of the dodecamer r(GAUCACUUCGGU) with four 5'-overhang nucleotides.
Acta Crystallogr.,Sect.D, 60:8-12, 2004

PubMed Abstract: The crystal structure of an RNA dodecamer, r(GAUCACUUCGGU), was solved at 2.6 A resolution by the molecular-replacement method and refined to an R(work) of 18.8% (R(free) = 22.8%) using 2494 reflections. The dodecamer crystallized in the monoclinic space group C2, with unit-cell parameters a = 71.34, b = 39.98, c = 32.47 A, beta = 104.7 degrees and two independent strands in the asymmetric unit. The dodecamer adopts an octamer duplex structure with four 5'-overhang residues (G1A2U3C4), which form Watson-Crick base pairs with another four 5'-overhang residues of a symmetry-related duplex. The octamer duplex (ACUUCGGU) contains at its center four mismatched base pairs flanked by two Watson-Crick base pairs. The mismatched bases form two G.U wobble base pairs at the ends and two U.C base pairs at the center, with one base-base hydrogen bond N4(C).O4(U) and a water bridge connecting the N(3) of the cytosine and uridine. The present study reinforces the concept of the stability of the conformation of UUCG in RNA double-helical structures.

PubMed: 14684886
DOI: 10.1107/S0907444903027860

Experimental method

X-RAY DIFFRACTION (2.6 Å)