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| Title | Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM. |
|---|---|
| Journal, issue, pages | Nucleic Acids Res, Vol. 51, Issue 18, Page 9952-9960, Year 2023 |
| Publish date | Oct 13, 2023 |
 Authors | Jienyu Ding / Justin C Deme / Jason R Stagno / Ping Yu / Susan M Lea / Yun-Xing Wang /  |
| PubMed Abstract | 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. |
 External links | Nucleic Acids Res / PubMed:37534568 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 3.0 - 5.3 Å |
| Structure data | EMDB-40262, PDB-8sa2: EMDB-40263, PDB-8sa3: EMDB-40264, PDB-8sa4: EMDB-40265, PDB-8sa5: EMDB-40266, PDB-8sa6: |
| Chemicals |  ChemComp-B1Z: |
| Source |
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 Keywords | RNA / RNA cobalamin riboswitch |
caldanaerobacter subterraneus subsp. tengcongensis (bacteria)