6cc1: Difference between revisions

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<StructureSection load='6cc1' size='340' side='right'caption='[[6cc1]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
<StructureSection load='6cc1' size='340' side='right'caption='[[6cc1]], [[Resolution|resolution]] 2.54&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6cc1]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CC1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6CC1 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6cc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Lactococcus_lactis Lactococcus lactis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CC1 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.54&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6cc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cc1 OCA], [http://pdbe.org/6cc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cc1 RCSB], [http://www.ebi.ac.uk/pdbsum/6cc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cc1 ProSAT]</span></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</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=6cc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cc1 OCA], [https://pdbe.org/6cc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cc1 RCSB], [https://www.ebi.ac.uk/pdbsum/6cc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cc1 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The large yybP-ykoY family of bacterial riboswitches is broadly distributed phylogenetically. Previously, these gene-regulatory RNAs were proposed to respond to Mn(2+). X-ray crystallography revealed a binuclear cation-binding pocket. This comprises one hexacoordinate site, with six oxygen ligands, which preorganizes the second, with five oxygen and one nitrogen ligands. The relatively soft nitrogen ligand was proposed to confer affinity for Mn(2+), but how this excludes other soft cations remained enigmatic. By subjecting representative yybP-ykoY riboswitches to diverse cations in vitro, we now find that these RNAs exhibit limited transition metal ion selectivity. Among the cations tested, Cd(2+) and Mn(2+) bind most tightly, and comparison of three new Cd(2+)-bound crystal structures suggests that these riboswitches achieve selectivity by enforcing heptacoordination (favored by high-spin Cd(2+) and Mn(2+), but otherwise uncommon) in the softer site. Remarkably, the Cd(2+)- and Mn(2+)-selective bacterial transcription factor MntR also uses heptacoordination within a binuclear site to achieve selectivity.


Convergent Use of Heptacoordination for Cation Selectivity by RNA and Protein Metalloregulators.,Bachas ST, Ferre-D'Amare AR Cell Chem Biol. 2018 May 4. pii: S2451-9456(18)30146-6. doi:, 10.1016/j.chembiol.2018.04.016. PMID:29805037<ref>PMID:29805037</ref>
==See Also==
 
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6cc1" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Lactococcus lactis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Bachas, S T]]
[[Category: Bachas ST]]
[[Category: Amare, A R.Ferre-D]]
[[Category: Ferre-D'amare AR]]
[[Category: Riboswich]]
[[Category: Rna]]
[[Category: Yybp-ykoy]]

Latest revision as of 17:27, 13 March 2024

Crystal structure of ykoY-alx riboswitch chimera bound to cadmiumCrystal structure of ykoY-alx riboswitch chimera bound to cadmium

Structural highlights

6cc1 is a 2 chain structure with sequence from Lactococcus lactis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.54Å
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

6cc1, resolution 2.54Å

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