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TitleCapturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.
Journal, issue, pagesNucleic Acids Res, Vol. 51, Issue 18, Page 9952-9960, Year 2023
Publish dateOct 13, 2023
AuthorsJienyu Ding / Justin C Deme / Jason R Stagno / Ping Yu / Susan M Lea / Yun-Xing Wang /
PubMed AbstractRNA 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 linksNucleic Acids Res / PubMed:37534568 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 5.3 Å
Structure data

EMDB-40262, PDB-8sa2:
Adenosylcobalamin-bound riboswitch dimer, form 1
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-40263, PDB-8sa3:
Adenosylcobalamin-bound riboswitch dimer, form 2
Method: EM (single particle) / Resolution: 3.0 Å

EMDB-40264, PDB-8sa4:
Adenosylcobalamin-bound riboswitch dimer, form 3
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-40265, PDB-8sa5:
Adenosylcobalamin-bound riboswitch dimer, form 4
Method: EM (single particle) / Resolution: 3.5 Å

EMDB-40266, PDB-8sa6:
apo form of adenosylcobalamin riboswitch dimer
Method: EM (single particle) / Resolution: 5.3 Å

Chemicals

ChemComp-B1Z:
Adenosylcobalamin / medication*YM

Source
  • caldanaerobacter subterraneus subsp. tengcongensis (bacteria)
KeywordsRNA / RNA cobalamin riboswitch

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