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==Crystal structure of an RNA aptamer in complex with fluorophore and Fab==
==Crystal structure of an RNA aptamer in complex with fluorophore and Fab==
<StructureSection load='4kzd' size='340' side='right' caption='[[4kzd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
<StructureSection load='4kzd' size='340' side='right'caption='[[4kzd]], [[Resolution|resolution]] 2.19&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4kzd]] is a 3 chain structure. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZD FirstGlance]. <br>
<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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1TU:4-(3,5-DIFLUORO-4-HYDROXYBENZYL)-1,2-DIMETHYL-1H-IMIDAZOL-5-OL'>1TU</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SUC:SUCROSE'>SUC</scene><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]] 2.186&#8491;</td></tr>
<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3ivk|3ivk]], [[4kze|4kze]]</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>
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kzd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kzd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kzd RCSB], [http://www.ebi.ac.uk/pdbsum/4kzd PDBsum]</span></td></tr>
</table>
<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&reg;/PubMed&reg;, 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__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Huang, H.]]
[[Category: Large Structures]]
[[Category: Koldobskaya, Y.]]
[[Category: Mus musculus]]
[[Category: Li, N.]]
[[Category: Huang H]]
[[Category: Piccirilli, J A.]]
[[Category: Koldobskaya Y]]
[[Category: Rice, P A.]]
[[Category: Li N]]
[[Category: Suslov, N B.]]
[[Category: Piccirilli JA]]
[[Category: Fluorescence]]
[[Category: Rice PA]]
[[Category: Fluorophore binding]]
[[Category: Suslov NB]]
[[Category: G-quadruplex]]
[[Category: Immune system-rna complex]]
[[Category: In vitro]]
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