2G3S

RNA structure containing GU base pairs

Summary for 2G3S

• Entry DOI: 10.2210/pdb2g3s/pdb
• Related: 1EKD
• Descriptor: 5'-R(*GP*GP*CP*GP*UP*GP*CP*C)-3', MAGNESIUM ION (3 entities in total)
• Functional Keywords: rna crystal structure, tandem gu base pairs, rna
• Biological source: synthetic construct
• Total number of polymer chains: 10
• Total formula weight: 25624.38

Authors

Jang, S.B.,Hung, L.W.,Jeong, M.S.,Holbrook, E.L.,Chen, X.,Turner, D.H.,Holbrook, S.R. (deposition date: 2006-02-20, release date: 2007-01-16, Last modification date: 2023-11-29)

Primary citation

Jang, S.B.,Hung, L.W.,Jeong, M.S.,Holbrook, E.L.,Chen, X.,Turner, D.H.,Holbrook, S.R.
The crystal structure at 1.5 angstroms resolution of an RNA octamer duplex containing tandem G.U basepairs
Biophys.J., 90:4530-4537, 2006

PubMed Abstract: The crystal structure of the RNA octamer, 5'-GGCGUGCC-3' has been determined from x-ray diffraction data to 1.5 angstroms resolution. In the crystal, this oligonucleotide forms five self-complementary double-helices in the asymmetric unit. Tandem 5'GU/3'UG basepairs comprise an internal loop in the middle of each duplex. The NMR structure of this octameric RNA sequence is also known, allowing comparison of the variation among the five crystallographic duplexes and the solution structure. The G.U pairs in the five duplexes of the crystal form two direct hydrogen bonds and are stabilized by water molecules that bridge between the base of guanine (N2) and the sugar (O2') of uracil. This contrasts with the NMR structure in which only one direct hydrogen bond is observed for the G.U pairs. The reduced stability of the r(CGUG)2 motif relative to the r(GGUC)2 motif may be explained by the lack of stacking of the uracil bases between the Watson-Crick and G.U pairs as observed in the crystal structure.

PubMed: 16581850
DOI: 10.1529/biophysj.106.081018

Experimental method

X-RAY DIFFRACTION (1.499 Å)