1nbk
From Proteopedia
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| - | [[Image:1nbk.gif|left|200px]]<br /><applet load="1nbk" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1nbk" /> | ||
| - | '''The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules'''<br /> | ||
| - | == | + | ==The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules== |
| + | <StructureSection load='1nbk' size='340' side='right'caption='[[1nbk]]' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1nbk]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NBK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NBK FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 1 model</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GND:2-AMINO-5-GUANIDINO-PENTANOIC+ACID'>GND</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=1nbk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nbk OCA], [https://pdbe.org/1nbk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nbk RCSB], [https://www.ebi.ac.uk/pdbsum/1nbk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nbk ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat. | An RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat. | ||
| - | + | Structural basis of the highly efficient trapping of the HIV Tat protein by an RNA aptamer.,Matsugami A, Kobayashi S, Ouhashi K, Uesugi S, Yamamoto R, Taira K, Nishikawa S, Kumar PK, Katahira M Structure. 2003 May;11(5):533-45. PMID:12737819<ref>PMID:12737819</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: | + | <div class="pdbe-citations 1nbk" style="background-color:#fffaf0;"></div> |
| - | [[Category: Katahira | + | == References == |
| - | [[Category: Kobayashi | + | <references/> |
| - | [[Category: Kumar | + | __TOC__ |
| - | [[Category: Matsugami | + | </StructureSection> |
| - | [[Category: Nishikawa | + | [[Category: Large Structures]] |
| - | [[Category: Ouhashi | + | [[Category: Katahira M]] |
| - | [[Category: Taira | + | [[Category: Kobayashi S]] |
| - | [[Category: Uesugi | + | [[Category: Kumar PKR]] |
| - | [[Category: Yamamoto | + | [[Category: Matsugami A]] |
| - | + | [[Category: Nishikawa S]] | |
| - | + | [[Category: Ouhashi K]] | |
| - | + | [[Category: Taira K]] | |
| - | + | [[Category: Uesugi S]] | |
| - | + | [[Category: Yamamoto R]] | |
| - | + | ||
| - | + | ||
Current revision
The structure of RNA aptamer for HIV Tat complexed with two argininamide molecules
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Categories: Large Structures | Katahira M | Kobayashi S | Kumar PKR | Matsugami A | Nishikawa S | Ouhashi K | Taira K | Uesugi S | Yamamoto R
