View source for 1vy4


==Crystal structure of the Thermus thermophilus 70S ribosome in the pre-attack state of peptide bond formation containing acylated tRNA-substrates in the A and P sites.==
<StructureSection load='1vy4' size='340' side='right'caption='[[1vy4]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vy4]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli], [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcm 4qcm], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcn 4qcn], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qco 4qco] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcp 4qcp]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VY4 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]] 2.6&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=31H:3-DEOXY-3-[(N-FORMYL-L-METHIONYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31H</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</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=F3N:3-DEOXY-3-(L-PHENYLALANYLAMINO)ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>F3N</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</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=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</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=1vy4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy4 OCA], [https://pdbe.org/1vy4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vy4 RCSB], [https://www.ebi.ac.uk/pdbsum/1vy4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vy4 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B]
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179<ref>PMID:25132179</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1vy4" style="background-color:#fffaf0;"></div>

==See Also==
*[[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: Escherichia coli]]
[[Category: Large Structures]]
[[Category: Synthetic construct]]
[[Category: Thermus thermophilus HB8]]
[[Category: Innis CA]]
[[Category: Polikanov YS]]
[[Category: Steitz TA]]