1n33

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[[Image:1n33.png|left|200px]]
 
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{{STRUCTURE_1n33| PDB=1n33 | SCENE= }}
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==Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin==
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<StructureSection load='1n33' size='340' side='right'caption='[[1n33]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1n33]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N33 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.35&#8491;</td></tr>
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<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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n33 OCA], [https://pdbe.org/1n33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n33 RCSB], [https://www.ebi.ac.uk/pdbsum/1n33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n33 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n33_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n33 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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A structural and mechanistic explanation for the selection of tRNAs by the ribosome has been elusive. Here, we report crystal structures of the 30S ribosomal subunit with codon and near-cognate tRNA anticodon stem loops bound at the decoding center and compare affinities of equivalent complexes in solution. In ribosomal interactions with near-cognate tRNA, deviation from Watson-Crick geometry results in uncompensated desolvation of hydrogen-bonding partners at the codon-anticodon minor groove. As a result, the transition to a closed form of the 30S induced by cognate tRNA is unfavorable for near-cognate tRNA unless paromomycin induces part of the rearrangement. We conclude that stabilization of a closed 30S conformation is required for tRNA selection, and thereby structurally rationalize much previous data on translational fidelity.
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===Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin===
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Selection of tRNA by the ribosome requires a transition from an open to a closed form.,Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V Cell. 2002 Nov 27;111(5):721-32. PMID:12464183<ref>PMID:12464183</ref>
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{{ABSTRACT_PUBMED_12464183}}
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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==About this Structure==
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<div class="pdbe-citations 1n33" style="background-color:#fffaf0;"></div>
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[[1n33]] is a 23 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N33 OCA].
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==See Also==
==See Also==
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*[[Ribosomal protein S10|Ribosomal protein S10]]
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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*[[Ribosomal protein S11|Ribosomal protein S11]]
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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*[[Ribosomal protein S12|Ribosomal protein S12]]
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== References ==
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*[[Ribosomal protein S13|Ribosomal protein S13]]
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<references/>
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*[[Ribosomal protein S14|Ribosomal protein S14]]
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__TOC__
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*[[Ribosomal protein S15|Ribosomal protein S15]]
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</StructureSection>
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*[[Ribosomal protein S16|Ribosomal protein S16]]
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[[Category: Large Structures]]
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*[[Ribosomal protein S17|Ribosomal protein S17]]
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*[[Ribosomal protein S18|Ribosomal protein S18]]
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*[[Ribosomal protein S19|Ribosomal protein S19]]
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*[[Ribosomal protein S2|Ribosomal protein S2]]
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*[[Ribosomal protein S20|Ribosomal protein S20]]
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*[[Ribosomal protein S3|Ribosomal protein S3]]
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*[[Ribosomal protein S4|Ribosomal protein S4]]
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*[[Ribosomal protein S5|Ribosomal protein S5]]
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*[[Ribosomal protein S6|Ribosomal protein S6]]
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*[[Ribosomal protein S7|Ribosomal protein S7]]
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*[[Ribosomal protein S8|Ribosomal protein S8]]
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*[[Ribosomal protein S9|Ribosomal protein S9]]
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*[[Ribosomal protein THX|Ribosomal protein THX]]
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*[[Ribosome|Ribosome]]
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==Reference==
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<ref group="xtra">PMID:012464183</ref><references group="xtra"/>
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: IV, F V.Murphy.]]
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[[Category: Murphy IV FV]]
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[[Category: Ogle, J M.]]
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[[Category: Ogle JM]]
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[[Category: Ramakrishnan, V.]]
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[[Category: Ramakrishnan V]]
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[[Category: Tarry, M J.]]
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[[Category: Tarry MJ]]
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[[Category: 30s ribosomal subunit]]
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[[Category: A site]]
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[[Category: Antibiotic]]
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[[Category: Anticodon]]
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[[Category: Codon]]
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[[Category: Decoding]]
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[[Category: G:u]]
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[[Category: Gu]]
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[[Category: Messenger rna]]
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[[Category: Mismatch]]
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[[Category: Mrna]]
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[[Category: Near-cognate]]
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[[Category: Paromomycin]]
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[[Category: Ribosome]]
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[[Category: Stem-loop]]
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[[Category: Transfer rna]]
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[[Category: Trna]]
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[[Category: Wobble]]
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Current revision

Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer rna anticodon stem-loop mismatched at the second codon position at the a site with paromomycin

PDB ID 1n33

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