4U92

Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad

4U92 の概要

• エントリーDOI: 10.2210/pdb4u92/pdb
• 分子名称: DNA (5'-D(*CP*CP*AP*KP*GP*CP*GP*TP*GP*G)-3'), BARIUM ION, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: dna quadruplex barium c-tetrad, dna
• 由来する生物種: synthetic construct
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 6460.32

構造登録者

Paukstelis, P.J.,Zhang, D.,Huang, T.,Lukeman, P. (登録日: 2014-08-05, 公開日: 2014-11-26, 最終更新日: 2023-12-27)

主引用文献

Zhang, D.,Huang, T.,Lukeman, P.S.,Paukstelis, P.J.
Crystal structure of a DNA/Ba2+ G-quadruplex containing a water-mediated C-tetrad.
Nucleic Acids Res., 42:13422-13429, 2014

PubMed Abstract: We have determined the 1.50 Å crystal structure of the DNA decamer, d(CCA(CNV)KGCGTGG) ((CNV)K, 3-cyanovinylcarbazole), which forms a G-quadruplex structure in the presence of Ba(2+). The structure contains several unique features including a bulged nucleotide and the first crystal structure observation of a C-tetrad. The structure reveals that water molecules mediate contacts between the divalent cations and the C-tetrad, allowing Ba(2+) ions to occupy adjacent steps in the central ion channel. One ordered Mg(2+) facilitates 3'-3' stacking of two quadruplexes in the asymmetric unit, while the bulged nucleotide mediates crystal contacts. Despite the high diffraction limit, the first four nucleotides including the (CNV)K nucleoside are disordered though they are still involved in crystal packing. This work suggests that the bulky hydrophobic groups may locally influence the formation of non-Watson-Crick structures from otherwise complementary sequences. These observations lead to the intriguing possibility that certain types of DNA damage may act as modulators of G-quadruplex formation.

PubMed: 25389267
DOI: 10.1093/nar/gku1122

実験手法

X-RAY DIFFRACTION (1.5 Å)