3rg5: Difference between revisions

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 ==Crystal Structure of Mouse tRNA(Sec)==
-<StructureSection load='3rg5' size='340' side='right' caption='[[3rg5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='3rg5' size='340' side='right'caption='[[3rg5]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3rg5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RG5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RG5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3rg5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RG5 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><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]] 2&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3rg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rg5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rg5 RCSB], [http://www.ebi.ac.uk/pdbsum/3rg5 PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<table>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3rg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rg5 OCA], [https://pdbe.org/3rg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rg5 RCSB], [https://www.ebi.ac.uk/pdbsum/3rg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rg5 ProSAT]</span></td></tr>
-<div style="background-color:#fffaf0;">
+</table>
-== Publication Abstract from PubMed ==
-BACKGROUND: Selenocysteine tRNAs (tRNA(Sec)) exhibit a number of unique identity elements that are recognized specifically by proteins of the selenocysteine biosynthetic pathways and decoding machineries. Presently, these identity elements and the mechanisms by which they are interpreted by tRNA(Sec)-interacting factors are incompletely understood. METHODOLOGY/PRINCIPAL FINDINGS: We applied rational mutagenesis to obtain well diffracting crystals of murine tRNA(Sec). tRNA(Sec) lacking the single-stranded 3'-acceptor end ((DeltaGCCA)RNA(Sec)) yielded a crystal structure at 2.0 A resolution. The global structure of (DeltaGCCA)RNA(Sec) resembles the structure of human tRNA(Sec) determined at 3.1 A resolution. Structural comparisons revealed flexible regions in tRNA(Sec) used for induced fit binding to selenophosphate synthetase. Water molecules located in the present structure were involved in the stabilization of two alternative conformations of the anticodon stem-loop. Modeling of a 2'-O-methylated ribose at position U34 of the anticodon loop as found in a sub-population of tRNA(Sec)in vivo showed how this modification favors an anticodon loop conformation that is functional during decoding on the ribosome. Soaking of crystals in Mn(2+)-containing buffer revealed eight potential divalent metal ion binding sites but the located metal ions did not significantly stabilize specific structural features of tRNA(Sec). CONCLUSIONS/SIGNIFICANCE: We provide the most highly resolved structure of a tRNA(Sec) molecule to date and assessed the influence of water molecules and metal ions on the molecule's conformation and dynamics. Our results suggest how conformational changes of tRNA(Sec) support its interaction with proteins.
-Crystal structure analysis reveals functional flexibility in the selenocysteine-specific tRNA from mouse.,Ganichkin OM, Anedchenko EA, Wahl MC PLoS One. 2011;6(5):e20032. Epub 2011 May 24. PMID:21629646<ref>PMID:21629646</ref>
-From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Anedchenko, E A.]]
+[[Category: Large Structures]]
-[[Category: Ganichkin, O M.]]
+[[Category: Mus musculus]]
-[[Category: Wahl, M C.]]
+[[Category: Anedchenko EA]]
-[[Category: Metal binding by rna]]
+[[Category: Ganichkin OM]]
-[[Category: Pstk]]
+[[Category: Wahl MC]]
-[[Category: Rna]]
-[[Category: Rna hydration]]
-[[Category: Sec]]
-[[Category: Serr]]
-[[Category: Structural flexibility]]
-[[Category: Translation]]
-[[Category: Trna fold]]
-[[Category: Trnasec]]