4wu1: Difference between revisions

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-'''Unreleased structure'''
-The entry 4wu1 is ON HOLD  until Paper Publication
+==Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site==
+<StructureSection load='4wu1' size='340' side='right'caption='[[4wu1]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4wu1]] is a 19 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=4WU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4WU1 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]] 3.2&#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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=QUO:2-AMINO-7-DEAZA-(2,3-DIHYDROXY-CYCLOPENTYLAMINO)-GUANOSINE-5-MONOPHOSPHATE'>QUO</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=4wu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4wu1 OCA], [https://pdbe.org/4wu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4wu1 RCSB], [https://www.ebi.ac.uk/pdbsum/4wu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4wu1 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity).[HAMAP-Rule:MF_01343]  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The decoding of mRNA on the ribosome is the least accurate process during genetic information transfer. Here we propose a unified decoding mechanism based on 11 high-resolution X-ray structures of the 70S ribosome that explains the occurrence of missense errors during translation. We determined ribosome structures in rare states where incorrect tRNAs were incorporated into the peptidyl-tRNA-binding site. These structures show that in the codon-anticodon duplex, a G.U mismatch adopts the Watson-Crick geometry, indicating a shift in the tautomeric equilibrium or ionization of the nucleobase. Additional structures with mismatches in the 70S decoding centre show that the binding of any tRNA induces identical rearrangements in the centre, which favours either isosteric or close to the Watson-Crick geometry codon-anticodon pairs. Overall, the results suggest that a mismatch escapes discrimination by preserving the shape of a Watson-Crick pair and indicate that geometric selection via tautomerism or ionization dominates the translational infidelity mechanism.
-Authors: Rozov, A., Demeshkina, N., Yusupov, M., Yusupova, G.
+Structural insights into the translational infidelity mechanism.,Rozov A, Demeshkina N, Westhof E, Yusupov M, Yusupova G Nat Commun. 2015 Jun 3;6:7251. doi: 10.1038/ncomms8251. PMID:26037619<ref>PMID:26037619</ref>
-Description: Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-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 4wu1" 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]]
+*[[Transfer RNA (tRNA)|Transfer RNA (tRNA)]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermus thermophilus HB8]]
+[[Category: Demeshkina N]]
+[[Category: Rozov A]]
+[[Category: Yusupov M]]
+[[Category: Yusupova G]]