8SA2

Adenosylcobalamin-bound riboswitch dimer, form 1

Summary for 8SA2

• Entry DOI: 10.2210/pdb8sa2/pdb
• EMDB information: 40262
• Descriptor: adenosylcobalamin riboswitch form 1, Adenosylcobalamin (2 entities in total)
• Functional Keywords: rna cobalamin riboswitch, rna
• Biological source: Caldanaerobacter subterraneus subsp. tengcongensis
• Total number of polymer chains: 2
• Total formula weight: 139708.51

Authors

Ding, J.,Deme, J.C.,Stagno, J.R.,Yu, P.,Lea, S.M.,Wang, Y.X. (deposition date: 2023-03-31, release date: 2023-07-26, Last modification date: 2023-10-25)

Primary citation

Ding, J.,Deme, J.C.,Stagno, J.R.,Yu, P.,Lea, S.M.,Wang, Y.X.
Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.
Nucleic Acids Res., 51:9952-9960, 2023

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 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.

PubMed: 37534568
DOI: 10.1093/nar/gkad651

Experimental method

ELECTRON MICROSCOPY (3.1 Å)