5fk4: Difference between revisions
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==SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UU== | ==SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UU== | ||
<StructureSection load='5fk4' size='340' side='right' caption='[[5fk4]], [[Resolution|resolution]] 2.43Å' scene=''> | <StructureSection load='5fk4' size='340' side='right'caption='[[5fk4]], [[Resolution|resolution]] 2.43Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5fk4]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FK4 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5fk4]] is a 1 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=5FK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FK4 FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.43Å</td></tr> | ||
<tr id=' | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=SAM:S-ADENOSYLMETHIONINE'>SAM</scene></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5fk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fk4 OCA], [https://pdbe.org/5fk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fk4 RCSB], [https://www.ebi.ac.uk/pdbsum/5fk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fk4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
| Line 21: | Line 21: | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: | [[Category: Caldanaerobacter subterraneus subsp. tengcongensis]] | ||
[[Category: Large Structures]] | |||
[[Category: | [[Category: Huang L]] | ||
[[Category: | [[Category: Lilley DMJ]] | ||
[[Category: | |||
Latest revision as of 14:40, 10 January 2024
SAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UUSAM-I riboswitch bearing the H. marismortui Kt-7 variant 3bn is UU
Structural highlights
Publication Abstract from PubMedk-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G*A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures. A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function.,Huang L, Wang J, Lilley DM Nucleic Acids Res. 2016 Mar 25. pii: gkw201. PMID:27016741[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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