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2oiy
From Proteopedia
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| - | [[Image:2oiy.jpg|left|200px]] | ||
| - | + | ==Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site== | |
| - | + | <StructureSection load='2oiy' size='340' side='right'caption='[[2oiy]], [[Resolution|resolution]] 1.60Å' scene=''> | |
| - | + | == Structural highlights == | |
| - | + | <table><tr><td colspan='2'>[[2oiy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OIY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OIY 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]] 1.6Å</td></tr> | |
| - | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=2oiy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oiy OCA], [https://pdbe.org/2oiy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oiy RCSB], [https://www.ebi.ac.uk/pdbsum/2oiy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oiy ProSAT]</span></td></tr> | |
| - | + | </table> | |
| - | + | <div style="background-color:#fffaf0;"> | |
| - | + | == Publication Abstract from PubMed == | |
| + | The crystal structure of subtype-B HIV-1 genomic RNA Dimerization Initiation Site duplex revealed chain cleavage at a specific position resulting in 3'-phosphate and 5'-hydroxyl termini. A crystallographic analysis showed that Ba(2+), Mn(2+), Co(2+) and Zn(2+) bind specifically on a guanine base close to the cleaved position. The crystal structures also point to a necessary conformational change to induce an 'in-line' geometry at the cleavage site. In solution, divalent cations increased the rate of cleavage with pH/pKa compensation, indicating that a cation-bound hydroxide anion is responsible for the cleavage. We propose a 'Trojan horse' mechanism, possibly of general interest, wherein a doubly charged cation hosted near the cleavage site as a 'harmless' species is further transformed in situ into an 'aggressive' species carrying a hydroxide anion. | ||
| - | + | Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.,Ennifar E, Walter P, Dumas P Nucleic Acids Res. 2010 Sep 1;38(17):5807-16. Epub 2010 May 11. PMID:20460458<ref>PMID:20460458</ref> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 2oiy" style="background-color:#fffaf0;"></div> | |
| - | [[Category: | + | == References == |
| - | [[Category: Dumas | + | <references/> |
| - | [[Category: Ennifar | + | __TOC__ |
| - | [[Category: Walter | + | </StructureSection> |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Dumas P]] | |
| - | + | [[Category: Ennifar E]] | |
| - | + | [[Category: Walter P]] | |
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Current revision
Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site
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