View source for 4v87


==Crystal structure analysis of ribosomal decoding.==
<StructureSection load='4v87' size='340' side='right'caption='[[4v87]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[4v87]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tve 3tve], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tvf 3tvf], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tvg 3tvg] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3tvh 3tvh]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4V87 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4V87 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4v87 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4v87 OCA], [https://pdbe.org/4v87 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4v87 RCSB], [https://www.ebi.ac.uk/pdbsum/4v87 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4v87 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RL17_THET8 RL17_THET8] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During protein synthesis, the ribosome accurately selects transfer RNAs (tRNAs) in accordance with the messenger RNA (mRNA) triplet in the decoding centre. tRNA selection is initiated by elongation factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre. At the following proofreading step the ribosome re-examines the tRNA and rejects it if it does not match the A codon. It was suggested that universally conserved G530, A1492 and A1493 of 16S ribosomal RNA, critical for tRNA binding in the A site, actively monitor cognate tRNA, and that recognition of the correct codon-anticodon duplex induces an overall ribosome conformational change (domain closure). Here we propose an integrated mechanism for decoding based on six X-ray structures of the 70S ribosome determined at 3.1-3.4 A resolution, modelling cognate or near-cognate states of the decoding centre at the proofreading step. We show that the 30S subunit undergoes an identical domain closure upon binding of either cognate or near-cognate tRNA. This conformational change of the 30S subunit forms a decoding centre that constrains the mRNA in such a way that the first two nucleotides of the A codon are limited to form Watson-Crick base pairs. When U.G and G.U mismatches, generally considered to form wobble base pairs, are at the first or second codon-anticodon position, the decoding centre forces this pair to adopt the geometry close to that of a canonical C.G pair. This by itself, or with distortions in the codon-anticodon mini-helix and the anticodon loop, causes the near-cognate tRNA to dissociate from the ribosome.

A new understanding of the decoding principle on the ribosome.,Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G Nature. 2012 Mar 21. doi: 10.1038/nature10913. PMID:22437501<ref>PMID:22437501</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4v87" style="background-color:#fffaf0;"></div>

==See Also==
*[[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: Jenner L]]
[[Category: Yusupov M]]
[[Category: Yusupova G]]