1n36: Difference between revisions

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New page: left|200px<br /><applet load="1n36" size="450" color="white" frame="true" align="right" spinBox="true" caption="1n36, resolution 3.65Å" /> '''Structure of the The...
 
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[[Image:1n36.gif|left|200px]]<br /><applet load="1n36" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1n36, resolution 3.65&Aring;" />
'''Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position'''<br />


==Overview==
==Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position==
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 load='1n36' size='340' side='right'caption='[[1n36]], [[Resolution|resolution]] 3.65&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1n36]] 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=1N36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N36 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]] 3.65&#8491;</td></tr>
<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=1n36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n36 OCA], [https://pdbe.org/1n36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n36 RCSB], [https://www.ebi.ac.uk/pdbsum/1n36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n36 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/n3/1n36_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=1n36 ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1N36 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 ZN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1N36 OCA].
*[[Ribosomal protein THX 3D structures|Ribosomal protein THX 3D structures]]
 
*[[Ribosome 3D structures|Ribosome 3D structures]]
==Reference==
__TOC__
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]
</StructureSection>
[[Category: Protein complex]]
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[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://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 21:55:21 2007''

Latest revision as of 10:51, 14 February 2024

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon positionStructure of the Thermus thermophilus 30S ribosomal subunit in the presence of crystallographically disordered codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position

Structural highlights

1n36 is a 10 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.65Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1n36, resolution 3.65Å

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