5ib8: Difference between revisions

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-'''Unreleased structure'''
-The entry 5ib8 is ON HOLD  until Paper Publication
+==Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site==
+<StructureSection load='5ib8' size='340' side='right'caption='[[5ib8]], [[Resolution|resolution]] 3.13&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5ib8]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IB8 FirstGlance]. <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]] 3.13&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=SPE:THERMINE'>SPE</scene>, <scene name='pdbligand=T6A:N-[N-(9-B-D-RIBOFURANOSYLPURIN-6-YL)CARBAMOYL]THREONINE-5-MONOPHOSPHATE'>T6A</scene>, <scene name='pdbligand=U8U:5-METHYLAMINOMETHYL-2-THIOURIDINE-5-MONOPHOSPHATE'>U8U</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=5ib8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ib8 OCA], [https://pdbe.org/5ib8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ib8 RCSB], [https://www.ebi.ac.uk/pdbsum/5ib8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ib8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Precise conversion of genetic information into proteins is essential to cellular health. However, a margin of error exists and is at its highest on the stage of translation of mRNA by the ribosome. Here we present three crystal structures of 70S ribosome complexes with messenger RNA and transfer RNAs and show that when a G*U base pair is at the first position of the codon-anticodon helix a conventional wobble pair cannot form because of inescapable steric clash between the guanosine of the A codon and the key nucleotide of decoding center adenosine 1493 of 16S rRNA. In our structure the rigid ribosomal decoding center, which is identically shaped for cognate or near-cognate tRNAs, forces this pair to adopt a geometry close to that of a canonical G*C pair. We further strengthen our hypothesis that spatial mimicry due either to base tautomerism or ionization dominates the translation infidelity mechanism.
-Authors: Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.
+The ribosome prohibits the G*U wobble geometry at the first position of the codon-anticodon helix.,Rozov A, Westhof E, Yusupov M, Yusupova G Nucleic Acids Res. 2016 May 12. pii: gkw431. PMID:27174928<ref>PMID:27174928</ref>
-Description: Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Yusupov, M]]
+<div class="pdbe-citations 5ib8" style="background-color:#fffaf0;"></div>
-[[Category: Rozov, A]]
-[[Category: Yusupova, G]]
+==See Also==
-[[Category: Demeshkina, N]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Demeshkina N]]
+[[Category: Rozov A]]
+[[Category: Yusupov M]]
+[[Category: Yusupova G]]