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New page: left|200px<br /> <applet load="1ddy" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ddy, resolution 3.0Å" /> '''MOLECULAR RECOGNITIO...
 
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[[Image:1ddy.gif|left|200px]]<br />
<applet load="1ddy" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ddy, resolution 3.0&Aring;" />
'''MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER'''<br />


==Overview==
==MOLECULAR RECOGNITION BY THE VITAMIN B12 RNA APTAMER==
Previous solution structures of ligand-binding RNA aptamers have shown, that molecular recognition is achieved by the folding of an initially, unstructured RNA around its cognate ligand, coupling the processes of RNA, folding and binding. The 3 A crystal structure of the cyanocobalamin, (vitamin B12) aptamer reported here suggests a different approach to, molecular recognition in which elements of RNA secondary structure combine, to create a solvent-accessible docking surface for a large, complex, ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a, duplex on this triplex creates a cleft that functions as the vitamin B12, binding site. Complementary packing of hydrophobic surfaces, direct, hydrogen bonding and dipolar interactions between the ligand and the RNA, appear to contribute to binding. The nature of the interactions that, stabilize complex formation and the possible uncoupling of folding and, binding for this RNA suggest a strong mechanistic similarity to typical, protein-ligand complexes.
<StructureSection load='1ddy' size='340' side='right'caption='[[1ddy]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ddy]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DDY 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]] 3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NME:METHYLAMINE'>NME</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=1ddy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddy OCA], [https://pdbe.org/1ddy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ddy RCSB], [https://www.ebi.ac.uk/pdbsum/1ddy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ddy ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Previous solution structures of ligand-binding RNA aptamers have shown that molecular recognition is achieved by the folding of an initially unstructured RNA around its cognate ligand, coupling the processes of RNA folding and binding. The 3 A crystal structure of the cyanocobalamin (vitamin B12) aptamer reported here suggests a different approach to molecular recognition in which elements of RNA secondary structure combine to create a solvent-accessible docking surface for a large, complex ligand. Central to this structure is a locally folding RNA triplex, stabilized by a novel three-stranded zipper. Perpendicular stacking of a duplex on this triplex creates a cleft that functions as the vitamin B12 binding site. Complementary packing of hydrophobic surfaces, direct hydrogen bonding and dipolar interactions between the ligand and the RNA appear to contribute to binding. The nature of the interactions that stabilize complex formation and the possible uncoupling of folding and binding for this RNA suggest a strong mechanistic similarity to typical protein-ligand complexes.


==About this Structure==
The structural basis for molecular recognition by the vitamin B 12 RNA aptamer.,Sussman D, Nix JC, Wilson C Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:10625428<ref>PMID:10625428</ref>
1DDY is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with B12 and NME as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DDY OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The structural basis for molecular recognition by the vitamin B 12 RNA aptamer., Sussman D, Nix JC, Wilson C, Nat Struct Biol. 2000 Jan;7(1):53-7. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10625428 10625428]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1ddy" style="background-color:#fffaf0;"></div>
[[Category: Nix, J.C.]]
== References ==
[[Category: Sussman, D.]]
<references/>
[[Category: Wilson, C.]]
__TOC__
[[Category: B12]]
</StructureSection>
[[Category: NME]]
[[Category: Large Structures]]
[[Category: aptamer]]
[[Category: Nix JC]]
[[Category: rna]]
[[Category: Sussman D]]
[[Category: triplex]]
[[Category: Wilson C]]
[[Category: vitamin b12]]
 
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