2fkx

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(New page: 200px<br /><applet load="2fkx" size="450" color="white" frame="true" align="right" spinBox="true" caption="2fkx" /> '''Ribosomal protein s15 from thermus thermophi...)
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[[Image:2fkx.jpg|left|200px]]<br /><applet load="2fkx" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2fkx" />
 
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'''Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure'''<br />
 
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==Overview==
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==Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure==
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The interaction between the ribosomal protein S15 and its binding sites in, the 16S RNA was examined from two points of view. First, the isolated, protein S15 was studied by comparing NMR conformer sets, available in the, PDB and recalculated using the CNS-ARIA protocol. Molecular dynamics (MD), trajectories were then recorded starting from a conformer of each set. The, recalculation of the S15 NMR structure, as well as the recording of MD, trajectories, reveals that several orientations of the N-terminal, alpha-helix alpha1 with respect to the structure core are populated. MD, trajectories of the complex between the ribosomal protein S15 and RNA were, also recorded in the presence and absence of Mg(2+) ions. The Mg(2+) ions, are hexacoordinated by water and RNA oxygens. The coordination spheres, mainly interact with the RNA phosphodiester backbone, reducing the RNA, mobility and inducing electrostatic screening. When the Mg(2+) ions are, removed, the internal mobility of the RNA and of the protein increases at, the interaction interface close to the RNA G-U/G-C motif as a result of a, gap between the phosphate groups in the UUCG capping tetraloop and of the, disruption of S15-RNA hydrogen bonds in that region. On the other hand, several S15-RNA hydrogen bonds are reinforced, and water bridges appear, between the three-way junction region and S15. The network of hydrogen, bonds observed in the loop between alpha1 and alpha2 is consequently, reorganized. In the absence of Mg(2+), this network has the same pattern, as the network observed in the isolated protein, where the helix alpha1 is, mobile with respect to the protein core. The presence of Mg(2+) ions may, thus play a role in stabilizing the orientation of the helix alpha1 of, S15.
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<StructureSection load='2fkx' size='340' side='right'caption='[[2fkx]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2fkx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FKX 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">Solution NMR</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=2fkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fkx OCA], [https://pdbe.org/2fkx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fkx RCSB], [https://www.ebi.ac.uk/pdbsum/2fkx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fkx ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS15_THETH RS15_THETH] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA. Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity).
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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/fk/2fkx_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2fkx ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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2FKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2FKX OCA].
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*[[Ribosomal protein S15|Ribosomal protein S15]]
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__TOC__
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==Reference==
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</StructureSection>
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The conformational landscape of the ribosomal protein S15 and its influence on the protein interaction with 16S RNA., Crety T, Malliavin TE, Biophys J. 2007 Apr 15;92(8):2647-65. Epub 2007 Jan 26. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=17259282 17259282]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Malliavin, T.E.]]
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[[Category: Malliavin TE]]
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[[Category: ribosomal protein]]
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[[Category: rna-binding protein]]
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[[Category: rrna-binding protein]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 10:36:41 2007''
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Current revision

Ribosomal protein s15 from thermus thermophilus, nmr recalculated structure

PDB ID 2fkx

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