1n33

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(New page: 200px<br /><applet load="1n33" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n33, resolution 3.35&Aring;" /> '''Structure of the The...)
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[[Image:1n33.gif|left|200px]]<br /><applet load="1n33" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1n33, resolution 3.35&Aring;" />
 
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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'''<br />
 
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==Overview==
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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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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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<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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==About this Structure==
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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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1N33 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with PAR, MG and ZN as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N33 OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12464183 12464183]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1n33" style="background-color:#fffaf0;"></div>
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[[Category: Thermus thermophilus]]
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[[Category: IV, F.V.Murphy.]]
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[[Category: Ogle, J.M.]]
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[[Category: Ramakrishnan, V.]]
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[[Category: Tarry, M.J.]]
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[[Category: MG]]
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[[Category: PAR]]
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[[Category: ZN]]
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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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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:54:44 2007''
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==See Also==
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*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
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*[[Ribosome 3D structures|Ribosome 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Thermus thermophilus]]
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[[Category: Murphy IV FV]]
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[[Category: Ogle JM]]
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[[Category: Ramakrishnan V]]
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[[Category: Tarry MJ]]

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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