6ck4: Difference between revisions

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 <StructureSection load='6ck4' size='340' side='right'caption='[[6ck4]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ck4]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CK4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CK4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ck4]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoanaerobacter_mathranii Thermoanaerobacter mathranii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CK4 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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]] 3.097&#8491;</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=6ck4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ck4 OCA], [http://pdbe.org/6ck4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ck4 RCSB], [http://www.ebi.ac.uk/pdbsum/6ck4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ck4 ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G4P:GUANOSINE-5,3-TETRAPHOSPHATE'>G4P</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=6ck4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ck4 OCA], [https://pdbe.org/6ck4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ck4 RCSB], [https://www.ebi.ac.uk/pdbsum/6ck4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ck4 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Two classes of riboswitches related to the ykkC guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the ykkC RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. ykkC aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the ykkC aptamer acquires new specificity represents a striking case of evolvability in RNA.
-Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.,Knappenberger AJ, Reiss CW, Strobel SA Elife. 2018 Jun 7;7. pii: 36381. doi: 10.7554/eLife.36381. PMID:29877798<ref>PMID:29877798</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6ck4" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Riboswitch 3D structures|Riboswitch 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Knappenberger, A J]]
+[[Category: Thermoanaerobacter mathranii]]
-[[Category: Reiss, C W]]
+[[Category: Knappenberger AJ]]
-[[Category: Strobel, S A]]
+[[Category: Reiss CW]]
-[[Category: Ppgpp]]
+[[Category: Strobel SA]]
-[[Category: Prpp]]
-[[Category: Riboswitch]]
-[[Category: Rna]]
-[[Category: Ykkc]]