National Institutes of Health/National Cancer Institute (NIH/NCI)
CCR Core Funding for Lea Group
米国
National Institutes of Health/National Cancer Institute (NIH/NCI)
CCR Core Funding for Wang Group
米国
引用
ジャーナル: Nucleic Acids Res / 年: 2023 タイトル: Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. 著者: Jienyu Ding / Justin C Deme / Jason R Stagno / Ping Yu / Susan M Lea / Yun-Xing Wang / 要旨: RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin ...RNA conformational heterogeneity often hampers its high-resolution structure determination, especially for large and flexible RNAs devoid of stabilizing proteins or ligands. The adenosylcobalamin riboswitch exhibits heterogeneous conformations under 1 mM Mg2+ concentration and ligand binding reduces conformational flexibility. Among all conformers, we determined one apo (5.3 Å) and four holo cryo-electron microscopy structures (overall 3.0-3.5 Å, binding pocket 2.9-3.2 Å). The holo dimers exhibit global motions of helical twisting and bending around the dimer interface. A backbone comparison of the apo and holo states reveals a large structural difference in the P6 extension position. The central strand of the binding pocket, junction 6/3, changes from an 'S'- to a 'U'-shaped conformation to accommodate ligand. Furthermore, the binding pocket can partially form under 1 mM Mg2+ and fully form under 10 mM Mg2+ within the bound-like structure in the absence of ligand. Our results not only demonstrate the stabilizing ligand-induced conformational changes in and around the binding pocket but may also provide further insight into the role of the P6 extension in ligand binding and selectivity.