4U37

Native 7mer-RNA duplex

Summary for 4U37

• Entry DOI: 10.2210/pdb4u37/pdb
• Related: 4U34 4U35 4U38
• Descriptor: RNA (5'-R(*UP*AP*GP*CP*UP*CP*C)-3'), RNA (5'-R(*GP*GP*AP*GP*CP*UP*A)-3') (3 entities in total)
• Functional Keywords: rna duplex, rna
• Biological source: synthetic construct; More
• Total number of polymer chains: 2
• Total formula weight: 4417.75

Authors

Sheng, J.,Larsen, A.,Heuberger, B.,Blain, J.C.,Szostak, J.W. (deposition date: 2014-07-18, release date: 2014-08-13, Last modification date: 2023-09-27)

Primary citation

Sheng, J.,Larsen, A.,Heuberger, B.D.,Blain, J.C.,Szostak, J.W.
Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs.
J.Am.Chem.Soc., 136:13916-13924, 2014

PubMed Abstract: Structural studies of modified nucleobases in RNA duplexes are critical for developing a full understanding of the stability and specificity of RNA base pairing. 2-Thio-uridine (s(2)U) is a modified nucleobase found in certain tRNAs. Thermodynamic studies have evaluated the effects of s(2)U on base pairing in RNA, where it has been shown to stabilize U:A pairs and destabilize U:G wobble pairs. Surprisingly, no high-resolution crystal structures of s(2)U-containing RNA duplexes have yet been reported. We present here two high-resolution crystal structures of heptamer RNA duplexes (5'-uagcs(2)Ucc-3' paired with 3'-aucgAgg-5' and with 3'-aucgUgg-5') containing s(2)U:A and s(2)U:U pairs, respectively. For comparison, we also present the structures of their native counterparts solved under identical conditions. We found that replacing O2 with S2 stabilizes the U:A base pair without any detectable structural perturbation. In contrast, an s(2)U:U base pair is strongly stabilized in one specific U:U pairing conformation out of four observed for the native U:U base pair. This s(2)U:U stabilization appears to be due at least in part to an unexpected sulfur-mediated hydrogen bond. This work provides additional insights into the effects of 2-thio-uridine on RNA base pairing.

PubMed: 25188906
DOI: 10.1021/ja508015a

Experimental method

X-RAY DIFFRACTION (1.55 Å)