8sa3: Difference between revisions
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==Adenosylcobalamin-bound riboswitch dimer, form 2== | |||
<StructureSection load='8sa3' size='340' side='right'caption='[[8sa3]], [[Resolution|resolution]] 3.00Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8sa3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Caldanaerobacter_subterraneus_subsp._tengcongensis Caldanaerobacter subterraneus subsp. tengcongensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8SA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8SA3 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3Å</td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8sa3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8sa3 OCA], [https://pdbe.org/8sa3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8sa3 RCSB], [https://www.ebi.ac.uk/pdbsum/8sa3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8sa3 ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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 A) and four holo cryo-electron microscopy structures (overall 3.0-3.5 A, binding pocket 2.9-3.2 A). 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. | |||
Capturing heterogeneous conformers of cobalamin riboswitch by cryo-EM.,Ding J, Deme JC, Stagno JR, Yu P, Lea SM, Wang YX Nucleic Acids Res. 2023 Oct 13;51(18):9952-9960. doi: 10.1093/nar/gkad651. PMID:37534568<ref>PMID:37534568</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 8sa3" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Riboswitch 3D structures|Riboswitch 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Caldanaerobacter subterraneus subsp. tengcongensis]] | |||
[[Category: Large Structures]] | |||
[[Category: Deme JC]] | |||
[[Category: Ding J]] | |||
[[Category: Lea SM]] | |||
[[Category: Stagno JR]] | |||
[[Category: Wang YX]] | |||
[[Category: Yu P]] | |||
Latest revision as of 06:18, 14 May 2025
Adenosylcobalamin-bound riboswitch dimer, form 2
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