2oj0: Difference between revisions

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[[Image:2oj0.png|left|200px]]


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==Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked==
The line below this paragraph, containing "STRUCTURE_2oj0", creates the "Structure Box" on the page.
<StructureSection load='2oj0' size='340' side='right'caption='[[2oj0]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[2oj0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OJ0 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
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<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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_2oj0|  PDB=2oj0  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj0 OCA], [https://pdbe.org/2oj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oj0 RCSB], [https://www.ebi.ac.uk/pdbsum/2oj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oj0 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.


===Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked===
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_20460458}}, adds the Publication Abstract to the page
<div class="pdbe-citations 2oj0" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 20460458 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_20460458}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2oj0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ0 OCA].
[[Category: Dumas P]]
 
[[Category: Ennifar E]]
==Reference==
[[Category: Walter P]]
<ref group="xtra">PMID:020460458</ref><references group="xtra"/>
[[Category: Dumas, P.]]
[[Category: Ennifar, E.]]
[[Category: Walter, P.]]
[[Category: Dimerization]]
[[Category: Di]]
[[Category: Hiv-1]]
[[Category: Metal ion]]
[[Category: Rna]]
Retrieved from "https://proteopedia.org/2oj0"