4kzd: Difference between revisions
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New page: '''Unreleased structure''' The entry 4kzd is ON HOLD until Paper Publication Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A. Description: |
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==Crystal structure of an RNA aptamer in complex with fluorophore and Fab== | |||
<StructureSection load='4kzd' size='340' side='right'caption='[[4kzd]], [[Resolution|resolution]] 2.19Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4kzd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KZD FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.186Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1TU:4-(3,5-DIFLUORO-4-HYDROXYBENZYL)-1,2-DIMETHYL-1H-IMIDAZOL-5-OL'>1TU</scene>, <scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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'>[https://proteopedia.org/fgij/fg.htm?mol=4kzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kzd OCA], [https://pdbe.org/4kzd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kzd RCSB], [https://www.ebi.ac.uk/pdbsum/4kzd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kzd ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-A and 2.4-A resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers. | |||
A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.,Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA Nat Chem Biol. 2014 Jun 22. doi: 10.1038/nchembio.1561. PMID:24952597<ref>PMID:24952597</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4kzd" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Antibody 3D structures|Antibody 3D structures]] | |||
*[[3D structures of non-human antibody|3D structures of non-human antibody]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Mus musculus]] | |||
[[Category: Huang H]] | |||
[[Category: Koldobskaya Y]] | |||
[[Category: Li N]] | |||
[[Category: Piccirilli JA]] | |||
[[Category: Rice PA]] | |||
[[Category: Suslov NB]] | |||
