2oj0: Difference between revisions

Line 1:

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

==Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked==

== Structural highlights ==

<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]. <br>

</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>

<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oiy|2oiy]], [[2oij|2oij]]</td></tr>

<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>

<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oj0 RCSB], [http://www.ebi.ac.uk/pdbsum/2oj0 PDBsum]</span></td></tr>

<table>

== 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>

~~The line below this paragraph~~, ~~containing "STRUCTURE_2oj0"~~, ~~creates the "Structure Box" on the page~~.

~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)

~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~

~~or leave the SCENE parameter empty for the default display~~.

-->

~~{{STRUCTURE_2oj0| PDB=2oj0 | SCENE= }}~~

~~===Crystal structure of the duplex form~~ of the ~~HIV-1(LAI) RNA dimerization initiation site MN soaked===~~

From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>

</div>

== References ==

~~<!--~~

~~The line below this paragraph, {{ABSTRACT_PUBMED_20460458}}, adds the Publication Abstract to the page~~

__TOC__

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 20460458 is the PubMed ID number~~.

</StructureSection>

-->

~~{{ABSTRACT_PUBMED_20460458}}~~

~~==About this Structure==~~

~~[[2oj0]] is a 2 chain structure. Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ0 OCA].~~

==~~Reference~~==

<~~ref group="xtra">PMID:020460458<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Dumas, P.]]

[[Category: Ennifar, E.]]

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools

@@ Line 1: / Line 1: @@
-[[Image:2oj0.png|left|200px]]
+==Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked==
+<StructureSection load='2oj0' size='340' side='right' caption='[[2oj0]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
+== Structural highlights ==
+<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]. <br>
+</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><br>
+<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2oiy|2oiy]], [[2oij|2oij]]</td></tr>
+<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glucokinase Glucokinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.2 2.7.1.2] </span></td></tr>
+<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oj0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oj0 RCSB], [http://www.ebi.ac.uk/pdbsum/2oj0 PDBsum]</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>
-The line below this paragraph, containing "STRUCTURE_2oj0", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_2oj0|  PDB=2oj0  |  SCENE=  }}
-===Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked===
+From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+</div>
+== References ==
-<!--
+<references/>
-The line below this paragraph, {{ABSTRACT_PUBMED_20460458}}, adds the Publication Abstract to the page
+__TOC__
-(as it appears on PubMed at http://www.pubmed.gov), where 20460458 is the PubMed ID number.
+</StructureSection>
--->
-{{ABSTRACT_PUBMED_20460458}}
-==About this Structure==
-[[2oj0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OJ0 OCA].
-==Reference==
-<ref group="xtra">PMID:020460458</ref><references group="xtra"/>
 [[Category: Dumas, P.]]
 [[Category: Ennifar, E.]]