1nkw: Difference between revisions

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-[[Image:1nkw.png|left|200px]]
-<!--
+==Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans==
-The line below this paragraph, containing "STRUCTURE_1nkw", creates the "Structure Box" on the page.
+<StructureSection load='1nkw' size='340' side='right'caption='[[1nkw]], [[Resolution|resolution]] 3.10&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'>[[1nkw]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1lnr 1lnr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kpj 1kpj] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc9 1kc9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NKW 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]] 3.1&#8491;</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=1nkw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nkw OCA], [https://pdbe.org/1nkw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nkw RCSB], [https://www.ebi.ac.uk/pdbsum/1nkw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nkw ProSAT]</span></td></tr>
-{{STRUCTURE_1nkw|  PDB=1nkw  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL2_DEIRA RL2_DEIRA] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_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/nk/1nkw_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=1nkw ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We describe the high resolution structure of the large ribosomal subunit from Deinococcus radiodurans (D50S), a gram-positive mesophile suitable for binding of antibiotics and functionally relevant ligands. The over-all structure of D50S is similar to that from the archae bacterium Haloarcula marismortui (H50S); however, a detailed comparison revealed significant differences, for example, in the orientation of nucleotides in peptidyl transferase center and in the structures of many ribosomal proteins. Analysis of ribosomal features involved in dynamic aspects of protein biosynthesis that are partially or fully disordered in H50S revealed the conformations of intersubunit bridges in unbound subunits, suggesting how they may change upon subunit association and how movements of the L1-stalk may facilitate the exit of tRNA.
-===Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans===
+High resolution structure of the large ribosomal subunit from a mesophilic eubacterium.,Harms J, Schluenzen F, Zarivach R, Bashan A, Gat S, Agmon I, Bartels H, Franceschi F, Yonath A Cell. 2001 Nov 30;107(5):679-88. PMID:11733066<ref>PMID:11733066</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_11733066}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1nkw" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11733066 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_11733066}}
-==About this Structure==
-[[1nkw]] is a 30 chain structure of [[Ribosomal protein L2]], [[Ribosomal protein L3]], [[Ribosomal protein L4]], [[Ribosomal protein L5]], [[Ribosomal protein L6]], [[Ribosomal protein L9]] and [[Ribosome]] with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. This structure supersedes the now removed PDB entries  and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1kc9 1kc9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NKW OCA].
 ==See Also==
-*[[Large Ribosomal Subunit of Haloarcula]]
+*[[Kink-turn motif|Kink-turn motif]]
-*[[Ribosomal protein L2]]
+*[[Large Ribosomal Subunit of Haloarcula|Large Ribosomal Subunit of Haloarcula]]
-*[[Ribosomal protein L3]]
+*[[Ribosome|Ribosome]]
-*[[Ribosomal protein L4]]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-*[[Ribosomal protein L5]]
+*[[User:Wayne Decatur/kink-turn motif|User:Wayne Decatur/kink-turn motif]]
-*[[Ribosomal protein L6]]
+== References ==
-*[[Ribosomal protein L9]]
+<references/>
-*[[Ribosome]]
+__TOC__
-*[[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit]]
+</StructureSection>
-*[[User:Wayne Decatur/kink-turn motif]]
-==Reference==
-<ref group="xtra">PMID:11733066</ref><references group="xtra"/>
 [[Category: Deinococcus radiodurans]]
-[[Category: Agmon, I.]]
+[[Category: Large Structures]]
-[[Category: Bartels, H.]]
+[[Category: Agmon I]]
-[[Category: Bashan, A.]]
+[[Category: Bartels H]]
-[[Category: Franceschi, F.]]
+[[Category: Bashan A]]
-[[Category: Gat, S.]]
+[[Category: Franceschi F]]
-[[Category: Harms, J M.]]
+[[Category: Gat S]]
-[[Category: Schluenzen, F.]]
+[[Category: Harms JM]]
-[[Category: Yonath, A.]]
+[[Category: Schluenzen F]]
-[[Category: Zarivach, R.]]
+[[Category: Yonath A]]
-[[Category: 50]]
+[[Category: Zarivach R]]
-[[Category: Deinococcus radioduran]]
-[[Category: Large subunit]]
-[[Category: Peptide bond formation]]
-[[Category: Peptidyl-transferase]]
-[[Category: Ribosome]]
-[[Category: X-ray structure]]