5uza: Difference between revisions

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<StructureSection load='5uza' size='340' side='right'caption='[[5uza]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
<StructureSection load='5uza' size='340' side='right'caption='[[5uza]], [[Resolution|resolution]] 2.22&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5uza]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5UZA FirstGlance]. <br>
<table><tr><td colspan='2'>[[5uza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZA FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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]] 2.22&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</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'>[http://proteopedia.org/fgij/fg.htm?mol=5uza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uza OCA], [http://pdbe.org/5uza PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uza RCSB], [http://www.ebi.ac.uk/pdbsum/5uza PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uza 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=5uza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uza OCA], [https://pdbe.org/5uza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uza RCSB], [https://www.ebi.ac.uk/pdbsum/5uza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uza ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Site-specific incorporation of labeled nucleotides is an extremely useful synthetic tool for many structural studies (e.g., NMR, electron paramagnetic resonance (EPR), fluorescence resonance energy transfer (FRET), and X-ray crystallography) of RNA. However, specific-position-labeled RNAs &gt;60 nt are not commercially available on a milligram scale. Position-selective labeling of RNA (PLOR) has been applied to prepare large RNAs labeled at desired positions, and all the required reagents are commercially available. Here, we present a step-by-step protocol for the solid-liquid hybrid phase method PLOR to synthesize 71-nt RNA samples with three different modification applications, containing (i) a (13)C(15)N-labeled segment; (ii) discrete residues modified with Cy3, Cy5, or biotin; or (iii) two iodo-U residues. The flexible procedure enables a wide range of downstream biophysical analyses using precisely localized functionalized nucleotides. All three RNAs were obtained in &lt;2 d, excluding time for preparing reagents and optimizing experimental conditions. With optimization, the protocol can be applied to other RNAs with various labeling schemes, such as ligation of segmentally labeled fragments.
Incorporation of isotopic, fluorescent, and heavy-atom-modified nucleotides into RNAs by position-selective labeling of RNA.,Liu Y, Holmstrom E, Yu P, Tan K, Zuo X, Nesbitt DJ, Sousa R, Stagno JR, Wang YX Nat Protoc. 2018 May;13(5):987-1005. doi: 10.1038/nprot.2018.002. Epub 2018 Apr, 12. PMID:29651055<ref>PMID:29651055</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5uza" 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: Large Structures]]
[[Category: Large Structures]]
[[Category: Liu, Y]]
[[Category: Vibrio vulnificus]]
[[Category: Stagno, J R]]
[[Category: Liu Y]]
[[Category: Wang, Y X]]
[[Category: Stagno JR]]
[[Category: Adenine riboswitch]]
[[Category: Wang Y-X]]
[[Category: Iodo-uridine]]
[[Category: Rna]]

Latest revision as of 14:30, 6 March 2024

Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)

5uza, resolution 2.22Å

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