4tzp: Difference between revisions
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==As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein== | ==As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein== | ||
<StructureSection load='4tzp' size='340' side='right' caption='[[4tzp]], [[Resolution|resolution]] 8.50Å' scene=''> | <StructureSection load='4tzp' size='340' side='right'caption='[[4tzp]], [[Resolution|resolution]] 8.50Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[4tzp]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TZP FirstGlance]. <br> | <table><tr><td colspan='2'>[[4tzp]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TZP FirstGlance]. <br> | ||
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lck|4lck]], [[4tzv|4tzv]], [[4tzw|4tzw]], [[4tzx|4tzx]], [[4tzy|4tzy]], [[4tzz|4tzz]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lck|4lck]], [[4tzv|4tzv]], [[4tzw|4tzw]], [[4tzx|4tzx]], [[4tzy|4tzy]], [[4tzz|4tzz]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rplGB, ybaB, ybxF, BSU01090 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=4tzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tzp OCA], [http://pdbe.org/4tzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tzp RCSB], [http://www.ebi.ac.uk/pdbsum/4tzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tzp ProSAT]</span></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=4tzp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tzp OCA], [http://pdbe.org/4tzp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tzp RCSB], [http://www.ebi.ac.uk/pdbsum/4tzp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tzp ProSAT]</span></td></tr> | ||
</table> | </table> | ||
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==See Also== | ==See Also== | ||
*[[ | *[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]] | ||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Vibrio subtilis ehrenberg 1835]] | |||
[[Category: Large Structures]] | |||
[[Category: Amare, A R.Ferre-D]] | [[Category: Amare, A R.Ferre-D]] | ||
[[Category: Zhang, J]] | [[Category: Zhang, J]] | ||
Revision as of 17:06, 10 May 2019
As Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF proteinAs Grown, Untreated Co-crystals of the Ternary Complex Containing a T-box Stem I RNA, its cognate tRNAGly, and B. subtilis YbxF protein
Structural highlights
Publication 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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