1n34: Difference between revisions

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-[[Image:1n34.gif|left|200px]]
- {{Structure
+==Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position==
-|PDB= 1n34 |SIZE=350|CAPTION= <scene name='initialview01'>1n34</scene>, resolution 3.80&Aring;
+<StructureSection load='1n34' size='340' side='right'caption='[[1n34]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ZN:ZINC ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1n34]] 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=1N34 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N34 FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1n34 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n34 OCA], [https://pdbe.org/1n34 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n34 RCSB], [https://www.ebi.ac.uk/pdbsum/1n34 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n34 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_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/n3/1n34_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1n34 ConSurf].
+<div style="clear:both"></div>
-'''Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position'''
+==See Also==
+*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-==Overview==
+__TOC__
-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.
+</StructureSection>
+[[Category: Large Structures]]
-==About this Structure==
-N34 is a [[Protein complex]] structure of sequences 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=1N34 OCA].
-==Reference==
-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://www.ncbi.nlm.nih.gov/pubmed/12464183 12464183]
-[[Category: Protein complex]]
 [[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: ZN]]
-[[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:51:30 2008''