3pdr: Difference between revisions

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<StructureSection load='3pdr' size='340' side='right'caption='[[3pdr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
<StructureSection load='3pdr' size='340' side='right'caption='[[3pdr]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3pdr]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PDR FirstGlance]. <br>
<table><tr><td colspan='2'>[[3pdr]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PDR FirstGlance]. <br>
</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=MN:MANGANESE+(II)+ION'>MN</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]] 1.853&#8491;</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=MN:MANGANESE+(II)+ION'>MN</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=3pdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pdr OCA], [https://pdbe.org/3pdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pdr RCSB], [https://www.ebi.ac.uk/pdbsum/3pdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pdr ProSAT]</span></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=3pdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pdr OCA], [https://pdbe.org/3pdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pdr RCSB], [https://www.ebi.ac.uk/pdbsum/3pdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pdr ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The M-box riboswitch couples intracellular magnesium levels to expression of bacterial metal transport genes. Structural analyses on other riboswitch RNA classes, which typically respond to a small organic metabolite, have revealed that ligand recognition occurs through a combination of base-stacking, electrostatic, and hydrogen-bonding interactions. In contrast, the M-box RNA triggers a change in gene expression upon association with an undefined population of metals, rather than responding to only a single ligand. Prior biophysical experimentation suggested that divalent ions associate with the M-box RNA to promote a compacted tertiary conformation, resulting in sequestration of a short sequence tract otherwise required for downstream gene expression. Electrostatic shielding from loosely associated metals is undoubtedly an important influence during this metal-mediated compaction pathway. However, it is also likely that a subset of divalent ions specifically occupies cation binding sites and promotes proper positioning of functional groups for tertiary structure stabilization. To better elucidate the role of these metal binding sites, we resolved a manganese-chelated M-box RNA complex to 1.86 A by X-ray crystallography. These data support the presence of at least eight well-ordered cation binding pockets, including several sites that had been predicted by biochemical studies but were not observed in prior structural analysis. Overall, these data support the presence of three metal-binding cores within the M-box RNA that facilitate a network of long-range interactions within the metal-bound, compacted conformation.
Insights into Metalloregulation by M-box Riboswitch RNAs via Structural Analysis of Manganese-Bound Complexes.,Ramesh A, Wakeman CA, Winkler WC J Mol Biol. 2011 Apr 8;407(4):556-70. Epub 2011 Feb 15. PMID:21315082<ref>PMID:21315082</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3pdr" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
*[[Riboswitch 3D structures|Riboswitch 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ramesh, A]]
[[Category: Ramesh A]]
[[Category: Winkler, W C]]
[[Category: Winkler WC]]
[[Category: Manganese-rna complex]]
[[Category: Rna]]

Latest revision as of 13:40, 21 February 2024

Crystal structure of manganese bound M-box RNACrystal structure of manganese bound M-box RNA

Structural highlights

3pdr is a 2 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.853Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

See Also

3pdr, resolution 1.85Å

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