5bjp: Difference between revisions
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==Crystal structure of the Corn RNA aptamer in complex with DFHO, iridium hexammine soak== | |||
<StructureSection load='5bjp' size='340' side='right' caption='[[5bjp]], [[Resolution|resolution]] 2.51Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5bjp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5BJP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5BJP FirstGlance]. <br> | |||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=747:(5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one'>747</scene>, <scene name='pdbligand=DMS:DIMETHYL+SULFOXIDE'>DMS</scene>, <scene name='pdbligand=IR:IRIDIUM+ION'>IR</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5bjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5bjp OCA], [http://pdbe.org/5bjp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5bjp RCSB], [http://www.ebi.ac.uk/pdbsum/5bjp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5bjp ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Corn, a 28-nucleotide RNA, increases yellow fluorescence of its cognate ligand 3,5-difluoro-4-hydroxybenzylidene-imidazolinone-2-oxime (DFHO) by >400-fold. Corn was selected in vitro to overcome limitations of other fluorogenic RNAs, particularly rapid photobleaching. We now report the Corn-DFHO co-crystal structure, discovering that the functional species is a quasisymmetric homodimer. Unusually, the dimer interface, in which six unpaired adenosines break overall two-fold symmetry, lacks any intermolecular base pairs. The homodimer encapsulates one DFHO at its interprotomer interface, sandwiching it with a G-quadruplex from each protomer. Corn and the green-fluorescent Spinach RNA are structurally unrelated. Their convergent use of G-quadruplexes underscores the usefulness of this motif for RNA-induced small-molecule fluorescence. The asymmetric dimer interface of Corn could provide a basis for the development of mutants that only fluoresce as heterodimers. Such variants would be analogous to Split GFP, and may be useful for analyzing RNA co-expression or association, or for designing self-assembling RNA nanostructures. | |||
A homodimer interface without base pairs in an RNA mimic of red fluorescent protein.,Warner KD, Sjekloca L, Song W, Filonov GS, Jaffrey SR, Ferre-D'Amare AR Nat Chem Biol. 2017 Sep 25. doi: 10.1038/nchembio.2475. PMID:28945234<ref>PMID:28945234</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 5bjp" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Amare, A R.Ferre-D]] | |||
[[Category: Filonov, G S]] | |||
[[Category: Jaffrey, S R]] | |||
[[Category: Song, W]] | |||
[[Category: Warner, K D]] | |||
[[Category: Aptamer]] | |||
[[Category: Fluorogenic rna]] | |||
[[Category: Rna]] | |||
