1n32: Difference between revisions

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-[[Image:1n32.png|left|200px]]
-<!--
+==Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin==
-The line below this paragraph, containing "STRUCTURE_1n32", creates the "Structure Box" on the page.
+<StructureSection load='1n32' size='340' side='right'caption='[[1n32]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1n32]] 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=1N32 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N32 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</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&#8491;</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=PAR:PAROMOMYCIN'>PAR</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1n32|  PDB=1n32  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1n32 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n32 OCA], [https://pdbe.org/1n32 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n32 RCSB], [https://www.ebi.ac.uk/pdbsum/1n32 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n32 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B]
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n3/1n32_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</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=1n32 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+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.
-===Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the first codon position at the a site with paromomycin===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_12464183}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1n32" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 12464183 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_12464183}}
-==About this Structure==
-[[1n32]] is a 23 chain structure of [[Ribosomal protein S10]], [[Ribosomal protein S11]], [[Ribosomal protein S12]], [[Ribosomal protein S13]], [[Ribosomal protein S15]], [[Ribosomal protein S17]], [[Ribosomal protein S2]], [[Ribosomal protein S20]], [[Ribosomal protein S3]], [[Ribosomal protein S4]], [[Ribosomal protein THX]] and [[Ribosome]] 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=1N32 OCA].
 ==See Also==
-*[[Ribosomal protein S10]]
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
-*[[Ribosomal protein S11]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein S12]]
+== References ==
-*[[Ribosomal protein S13]]
+<references/>
-*[[Ribosomal protein S15]]
+__TOC__
-*[[Ribosomal protein S17]]
+</StructureSection>
-*[[Ribosomal protein S2]]
+[[Category: Large Structures]]
-*[[Ribosomal protein S20]]
-*[[Ribosomal protein S3]]
-*[[Ribosomal protein S4]]
-*[[Ribosomal protein THX]]
-*[[Ribosome]]
-==Reference==
-<ref group="xtra">PMID:12464183</ref><references group="xtra"/>
 [[Category: Thermus thermophilus]]
-[[Category: IV, F V.Murphy.]]
+[[Category: Murphy IV FV]]
-[[Category: Ogle, J M.]]
+[[Category: Ogle JM]]
-[[Category: Ramakrishnan, V.]]
+[[Category: Ramakrishnan V]]
-[[Category: Tarry, M J.]]
+[[Category: Tarry MJ]]
-[[Category: 30s ribosomal subunit]]
-[[Category: A site]]
-[[Category: Antibiotic]]
-[[Category: Anticodon]]
-[[Category: Codon]]
-[[Category: Decoding]]
-[[Category: G:u]]
-[[Category: Gu]]
-[[Category: Messenger rna]]
-[[Category: Mismatch]]
-[[Category: Mrna]]
-[[Category: Near-cognate]]
-[[Category: Paromomycin]]
-[[Category: Ribosome]]
-[[Category: Stem-loop]]
-[[Category: Transfer rna]]
-[[Category: Trna]]
-[[Category: Wobble]]