7eol
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==Crystal structure of the Pepper aptamer in complex with HBC497== | ==Crystal structure of the Pepper aptamer in complex with HBC497== | ||
| - | <StructureSection load='7eol' size='340' side='right'caption='[[7eol]]' scene=''> | + | <StructureSection load='7eol' size='340' side='right'caption='[[7eol]], [[Resolution|resolution]] 2.31Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EOL FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[7eol]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EOL FirstGlance]. <br> |
| - | </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=7eol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eol OCA], [https://pdbe.org/7eol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eol RCSB], [https://www.ebi.ac.uk/pdbsum/7eol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eol ProSAT]</span></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.309Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=J8O:4-[(~{Z})-1-cyano-2-[5-[2-hydroxyethyl(methyl)amino]pyrazin-2-yl]ethenyl]benzenecarbonitrile'>J8O</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7eol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eol OCA], [https://pdbe.org/7eol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eol RCSB], [https://www.ebi.ac.uk/pdbsum/7eol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eol ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | Pepper fluorescent RNAs are a recently reported bright, stable and multicolor fluorogenic aptamer tag that enable imaging of diverse RNAs in live cells. To investigate the molecular basis of the superior properties of Pepper, we determined the structures of complexes of Pepper aptamer bound with its cognate HBC or HBC-like fluorophores at high resolution by X-ray crystallography. The Pepper aptamer folds in a monomeric non-G-quadruplex tuning-fork-like architecture composed of a helix and one protruded junction region. The near-planar fluorophore molecule intercalates in the middle of the structure and is sandwiched between one non-G-quadruplex base quadruple and one noncanonical G.U wobble helical base pair. In addition, structure-based mutational analysis is evaluated by in vitro and live-cell fluorogenic detection. Taken together, our research provides a structural basis for demystifying the fluorescence activation mechanism of Pepper aptamer and for further improvement of its future application in RNA visualization. | ||
| + | |||
| + | Structure-based investigation of fluorogenic Pepper aptamer.,Huang K, Chen X, Li C, Song Q, Li H, Zhu L, Yang Y, Ren A Nat Chem Biol. 2021 Dec;17(12):1289-1295. doi: 10.1038/s41589-021-00884-6. Epub, 2021 Nov 1. PMID:34725509<ref>PMID:34725509</ref> | ||
| + | |||
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| + | </div> | ||
| + | <div class="pdbe-citations 7eol" style="background-color:#fffaf0;"></div> | ||
| + | == References == | ||
| + | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
| + | [[Category: Synthetic construct]] | ||
[[Category: Huang KY]] | [[Category: Huang KY]] | ||
[[Category: Ren AM]] | [[Category: Ren AM]] | ||
Current revision
Crystal structure of the Pepper aptamer in complex with HBC497
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