4rgf: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
 ==Crystal structure of the in-line aligned env22 twister ribozyme soaked with Mn2+==
-<StructureSection load='4rgf' size='340' side='right' caption='[[4rgf]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+<StructureSection load='4rgf' size='340' side='right'caption='[[4rgf]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rgf]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RGF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 3.2008&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DU:2-DEOXYURIDINE-5-MONOPHOSPHATE'>DU</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rge|4rge]]</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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [https://pdbe.org/4rgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [https://www.ebi.ac.uk/pdbsum/4rgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rgf 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=4rgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rgf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rgf RCSB], [http://www.ebi.ac.uk/pdbsum/4rgf PDBsum]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Small self-cleaving nucleolytic ribozymes contain catalytic domains that accelerate site-specific cleavage/ligation of phosphodiester backbones. We report on the 2.9-A crystal structure of the env22 twister ribozyme, which adopts a compact tertiary fold stabilized by co-helical stacking, double-pseudoknot formation and long-range pairing interactions. The U-A cleavage site adopts a splayed-apart conformation with the modelled 2'-O of U positioned for in-line attack on the adjacent to-be-cleaved P-O5' bond. Both an invariant guanosine and a Mg(2+) are directly coordinated to the non-bridging phosphate oxygens at the U-A cleavage step, with the former positioned to contribute to catalysis and the latter to structural integrity. The impact of key mutations on cleavage activity identified an invariant guanosine that contributes to catalysis. Our structure of the in-line aligned env22 twister ribozyme is compared with two recently reported twister ribozymes structures, which adopt similar global folds, but differ in conformational features around the cleavage site.
-In-line alignment and Mg(2+) coordination at the cleavage site of the env22 twister ribozyme.,Ren A, Kosutic M, Rajashankar KR, Frener M, Santner T, Westhof E, Micura R, Patel DJ Nat Commun. 2014 Nov 20;5:5534. doi: 10.1038/ncomms6534. PMID:25410397<ref>PMID:25410397</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Ribozyme 3D structures|Ribozyme 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Patel, D]]
+[[Category: Large Structures]]
-[[Category: Rajashankar, K R]]
+[[Category: Synthetic construct]]
-[[Category: Ren, A]]
+[[Category: Patel D]]
-[[Category: Simanshu, D]]
+[[Category: Rajashankar KR]]
-[[Category: Cleavage]]
+[[Category: Ren A]]
-[[Category: Pseudoknot]]
+[[Category: Simanshu D]]
-[[Category: Rna]]
-[[Category: Stem]]