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4tzz

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Revision as of 07:53, 22 March 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 and increasing PEG3350 concentration from 20% to 45% post crystallization

Structural highlights

4tzz is a 12 chain structure with sequence from Bacillus subtilis and Oceanobacillus iheyensis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RXL7_BACSU

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Zhang J, Ferre-D'Amare AR. Dramatic Improvement of Crystals of Large RNAs by Cation Replacement and Dehydration. Structure. 2014 Sep 2;22(9):1363-71. doi: 10.1016/j.str.2014.07.011. PMID:25185828 doi:http://dx.doi.org/10.1016/j.str.2014.07.011

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4tzz"

Categories: Bacillus subtilis | Large Structures | Oceanobacillus iheyensis | Ferre-D'Amare AR | Zhang J

@@ Line 3: / Line 3: @@
 <StructureSection load='4tzz' size='340' side='right'caption='[[4tzz]], [[Resolution|resolution]] 3.64&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4tzz]] is a 12 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=4TZZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4TZZ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4tzz]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] and [https://en.wikipedia.org/wiki/Oceanobacillus_iheyensis Oceanobacillus iheyensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4TZZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4TZZ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4tzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tzz OCA], [https://pdbe.org/4tzz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4tzz RCSB], [https://www.ebi.ac.uk/pdbsum/4tzz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4tzz ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lck|4lck]], [[4tzp|4tzp]], [[4tzv|4tzv]], [[4tzw|4tzw]], [[4tzx|4tzx]], [[4tzy|4tzy]]</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=4tzz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4tzz OCA], [http://pdbe.org/4tzz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4tzz RCSB], [http://www.ebi.ac.uk/pdbsum/4tzz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4tzz ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/RXL7_BACSU RXL7_BACSU]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Vibrio subtilis ehrenberg 1835]]
+[[Category: Bacillus subtilis]]
 [[Category: Large Structures]]
-[[Category: Amare, A R.Ferre-D]]
+[[Category: Oceanobacillus iheyensis]]
-[[Category: Zhang, J]]
+[[Category: Ferre-D'Amare AR]]
-[[Category: Ribosomal protein-rna complex]]
+[[Category: Zhang J]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: T-box]]
-[[Category: Trna]]

4tzz

From Proteopedia

Revision as of 07:53, 22 March 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 and increasing PEG3350 concentration from 20% to 45% post crystallization

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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