4tzv: Difference between revisions
New page: '''Unreleased structure''' The entry 4tzv is ON HOLD Authors: Zhang, J., Ferre-D'Amare, A.R. Description: Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate ... |
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==Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization== | |||
<StructureSection load='4tzv' size='340' side='right'caption='[[4tzv]], [[Resolution|resolution]] 5.03Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4tzv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis_HTE831 Oceanobacillus iheyensis HTE831]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TZV FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 5.03Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4tzv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tzv OCA], [https://pdbe.org/4tzv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tzv RCSB], [https://www.ebi.ac.uk/pdbsum/4tzv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tzv ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RXL7_BACSU RXL7_BACSU] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Compared to globular proteins, RNAs with complex 3D folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a postcrystallization treatment strategy that exploits the importance of solvation and counterions for RNA folding. Replacement of Li(+) and Mg(2+) needed for growth of crystals of a tRNA-riboswitch-protein complex with Sr(2+), coupled with dehydration, dramatically improved the resolution limit (8.5-3.2 A) and data quality, enabling structure determination. The soft Sr(2+) ion forms numerous stabilizing intermolecular contacts. Comparison of pre- and posttreatment structures reveals how RNA assemblies redistribute as quasi-rigid bodies to yield improved crystal packing. Cation exchange complements previously reported postcrystallization dehydration of protein crystals and represents a potentially general strategy for improving crystals of large RNAs. | |||
Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.,Zhang J, Ferre-D'Amare AR Structure. 2014 Sep 2;22(9):1363-71. doi: 10.1016/j.str.2014.07.011. PMID:25185828<ref>PMID:25185828</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4tzv" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bacillus subtilis]] | |||
[[Category: Large Structures]] | |||
[[Category: Oceanobacillus iheyensis HTE831]] | |||
[[Category: Ferre-D'Amare AR]] | |||
[[Category: Zhang J]] | |||
Latest revision as of 10:24, 27 September 2023
Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallizationCo-crystals of the Ternary Complex Containing a T-box Stem I RNA, its Cognate tRNAGly, and B. subtilis YbxF protein, treated by removing lithium sulfate post crystallization
Structural highlights
FunctionPublication Abstract from PubMedCompared to globular proteins, RNAs with complex 3D folds are characterized by poorly differentiated molecular surfaces dominated by backbone phosphates, sparse tertiary contacts stabilizing global architecture, and conformational flexibility. The resulting generally poor order of crystals of large RNAs and their complexes frequently hampers crystallographic structure determination. We describe and rationalize a postcrystallization treatment strategy that exploits the importance of solvation and counterions for RNA folding. Replacement of Li(+) and Mg(2+) needed for growth of crystals of a tRNA-riboswitch-protein complex with Sr(2+), coupled with dehydration, dramatically improved the resolution limit (8.5-3.2 A) and data quality, enabling structure determination. The soft Sr(2+) ion forms numerous stabilizing intermolecular contacts. Comparison of pre- and posttreatment structures reveals how RNA assemblies redistribute as quasi-rigid bodies to yield improved crystal packing. Cation exchange complements previously reported postcrystallization dehydration of protein crystals and represents a potentially general strategy for improving crystals of large RNAs. Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration.,Zhang J, Ferre-D'Amare AR Structure. 2014 Sep 2;22(9):1363-71. doi: 10.1016/j.str.2014.07.011. PMID:25185828[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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