6db8: Difference between revisions

Latest revision as of 15:21, 4 October 2023

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

Structural highlights

6db8 is a 3 chain structure with sequence from Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8654134Å
Ligands:	G4A
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO3 bound forms of DIR2s at 2.0 A and 1.8 A resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.,Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA Nat Commun. 2018 Oct 31;9(1):4542. doi: 10.1038/s41467-018-06942-3. PMID:30382099^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun. 2018 Oct 31;9(1):4542. doi: 10.1038/s41467-018-06942-3. PMID:30382099 doi:https://dx.doi.org/10.1038/s41467-018-06942-3

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Shelke SA, Shao Y, Laski A, Koirala D, Weissman BP, Fuller JR, Tan X, Constantin TP, Waggoner AS, Bruchez MP, Armitage BA, Piccirilli JA. Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif. Nat Commun. 2018 Oct 31;9(1):4542. doi: 10.1038/s41467-018-06942-3. PMID:30382099 doi:https://dx.doi.org/10.1038/s41467-018-06942-3

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6db8' size='340' side='right'caption='[[6db8]], [[Resolution|resolution]] 1.87&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6db8]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6db8]] is a 3 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=6DB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DB8 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</scene></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]] 1.8654134&#8491;</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=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [http://pdbe.org/6db8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [http://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4A:2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium'>G4A</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=6db8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6db8 OCA], [https://pdbe.org/6db8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6db8 RCSB], [https://www.ebi.ac.uk/pdbsum/6db8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6db8 ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 21: / Line 22: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Synthetic construct sequences]]
+[[Category: Synthetic construct]]
-[[Category: Laski, A]]
+[[Category: Laski A]]
-[[Category: Piccirilli, J A]]
+[[Category: Piccirilli JA]]
-[[Category: Shao, Y]]
+[[Category: Shao Y]]
-[[Category: Shelke, S A]]
+[[Category: Shelke SA]]
-[[Category: Dir]]
-[[Category: Fab]]
-[[Category: Fluorescent aptamer]]
-[[Category: Rna]]
-[[Category: Rna-immune system complex]]

6db8: Difference between revisions

Latest revision as of 15:21, 4 October 2023

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer

Structural highlights

Publication Abstract from PubMed

References

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