4enb: Difference between revisions

Line 1:

[[~~Image~~:~~4enb~~.~~png~~|~~left~~|~~200px~~]]

==Crystal structure of fluoride riboswitch, bound to Iridium==

== Structural highlights ==

<table><tr><td colspan='2'>[[4enb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ENB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ENB FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4enb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4enb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4enb RCSB], [http://www.ebi.ac.uk/pdbsum/4enb PDBsum]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A*U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.

~~{{STRUCTURE_4enb| PDB=4enb | SCENE= }}~~

Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.,Ren A, Rajashankar KR, Patel DJ Nature. 2012 May 13;486(7401):85-9. doi: 10.1038/nature11152. PMID:22678284<ref>PMID:22678284</ref>

~~===Crystal structure~~ of ~~fluoride riboswitch, bound to Iridium===~~

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

</div>

~~{{ABSTRACT_PUBMED_22678284}}~~

==See Also==

*[[Riboswitch|Riboswitch]]

==~~About this Structure~~==

== References ==

[[~~4enb~~]] ~~is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ENB OCA].~~

__TOC__

==~~Reference~~==

</StructureSection>

<~~ref group="xtra">PMID:022678284<~~/~~ref~~><~~references group="xtra"~~/>

[[Category: Patel, D J]]

[[Category: Patel, D J.]]

[[Category: Rajashankar, K R]]

[[Category: Rajashankar, K R.]]

[[Category: Ren, A M]]

[[Category: Ren, A M.]]

[[Category: Pseudoknot]]

[[Category: Rna]]

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@@ Line 1: / Line 1: @@
-[[Image:4enb.png|left|200px]]
+==Crystal structure of fluoride riboswitch, bound to Iridium==
+<StructureSection load='4enb' size='340' side='right' caption='[[4enb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4enb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ENB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ENB FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=IRI:IRIDIUM+HEXAMMINE+ION'>IRI</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4en5|4en5]], [[4ena|4ena]], [[4enc|4enc]], [[3vrs|3vrs]]</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4enb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4enb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4enb RCSB], [http://www.ebi.ac.uk/pdbsum/4enb PDBsum]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A*U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.
-{{STRUCTURE_4enb|  PDB=4enb  |  SCENE=  }}
+Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.,Ren A, Rajashankar KR, Patel DJ Nature. 2012 May 13;486(7401):85-9. doi: 10.1038/nature11152. PMID:22678284<ref>PMID:22678284</ref>
-===Crystal structure of fluoride riboswitch, bound to Iridium===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-{{ABSTRACT_PUBMED_22678284}}
+==See Also==
+*[[Riboswitch|Riboswitch]]
-==About this Structure==
+== References ==
-[[4enb]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ENB OCA].
+<references/>
+__TOC__
-==Reference==
+</StructureSection>
-<ref group="xtra">PMID:022678284</ref><references group="xtra"/>
+[[Category: Patel, D J]]
-[[Category: Patel, D J.]]
+[[Category: Rajashankar, K R]]
-[[Category: Rajashankar, K R.]]
+[[Category: Ren, A M]]
-[[Category: Ren, A M.]]
 [[Category: Pseudoknot]]
 [[Category: Rna]]