2k3f: Difference between revisions

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 ==Ribosomal protein L11 from Thermotoga maritima==
-<StructureSection load='2k3f' size='340' side='right' caption='[[2k3f]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2k3f' size='340' side='right'caption='[[2k3f]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2k3f]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K3F OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2K3F FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2k3f]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima Thermotoga maritima]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2K3F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2K3F FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rplK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2336 Thermotoga maritima])</td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2k3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k3f OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2k3f RCSB], [http://www.ebi.ac.uk/pdbsum/2k3f PDBsum]</span></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=2k3f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2k3f OCA], [https://pdbe.org/2k3f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2k3f RCSB], [https://www.ebi.ac.uk/pdbsum/2k3f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2k3f ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RL11_THEMA RL11_THEMA]] This protein binds directly to 23S ribosomal RNA.
+[https://www.uniprot.org/uniprot/RL11_THEMA RL11_THEMA] This protein binds directly to 23S ribosomal RNA.
 == 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/k3/2k3f_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/k3/2k3f_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2k3f ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-L11, a protein of the large ribosomal subunit, binds to a highly conserved domain of 23S rRNA and mediates ribosomal GTPase activity. Its C-terminal domain is the main determinant for rRNA binding, whereas its N-terminal domain plays only a limited role in RNA binding. The N-terminal domain is thought to be involved in interactions with elongation and release factors as well as with the antibiotics thiostrepton and micrococcin. This report presents the NMR solution structure of the full-length L11 protein from the thermophilic eubacterium Thermotoga maritima in its free form. The structure is based on a large number of orientational restraints derived from residual dipolar couplings in addition to conventional NOE-based restraints. The solution structure of L11 demonstrates that, in contrast to many other multidomain RNA-binding proteins, the relative orientation of the two domains is well defined. This is shown both by heteronuclear 15N-relaxation and residual dipolar-coupling data. Comparison of this NMR structure with the X-ray structure of RNA-bound L11, reveals that binding not only induces a rigidification of a flexible loop in the C-terminal domain, but also a sizeable reorientation of the N-terminal domain. The domain orientation in free L11 shows limited similarity to that of ribosome-bound L11 in complex with elongation factor, EF-G.
-Domain reorientation and induced fit upon RNA binding: solution structure and dynamics of ribosomal protein L11 from Thermotoga maritima.,Ilin S, Hoskins A, Ohlenschlager O, Jonker HR, Schwalbe H, Wohnert J Chembiochem. 2005 Sep;6(9):1611-8. PMID:16094695<ref>PMID:16094695</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+==See Also==
-</div>
+*[[Ribosomal protein L11 3D structures|Ribosomal protein L11 3D structures]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermotoga maritima]]
-[[Category: Ilin, S]]
+[[Category: Ilin S]]
-[[Category: Jonker, H R.A]]
+[[Category: Jonker HRA]]
-[[Category: Schwalbe, H]]
+[[Category: Schwalbe H]]
-[[Category: Woehnert, J]]
+[[Category: Woehnert J]]
-[[Category: L11]]
-[[Category: Methylation]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Rna-binding]]