2ogn: Difference between revisions

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-[[Image:2ogn.png|left|200px]]
-<!--
+==The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080==
-The line below this paragraph, containing "STRUCTURE_2ogn", creates the "Structure Box" on the page.
+<StructureSection load='2ogn' size='340' side='right'caption='[[2ogn]], [[Resolution|resolution]] 3.56&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'>[[2ogn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OGN 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]] 3.56&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=G80:(3AS,4R,5S,6S,8R,9R,9AR,10R)-5-HYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROPANOCYCLOPENTA[8]ANNULEN-8-YL+(PIPERIDIN-4-YLTHIO)ACETATE'>G80</scene></td></tr>
-{{STRUCTURE_2ogn|  PDB=2ogn  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2ogn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ogn OCA], [https://pdbe.org/2ogn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ogn RCSB], [https://www.ebi.ac.uk/pdbsum/2ogn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ogn ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL3_DEIRA RL3_DEIRA] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_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/og/2ogn_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=2ogn ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+New insights into functional flexibility at the peptidyl transferase center (PTC) and its vicinity were obtained by analysis of pleuromutilins binding modes to the ribosome. The crystal structures of Deinococcus radiodurans large ribosomal subunit complexed with each of three pleuromutilin derivatives: retapamulin (SB-275833), SB-280080, and SB-571519, show that all bind to the PTC with their core oriented similarly at the A-site and their C14 extensions pointing toward the P-site. Except for an H-bond network with a single nucleotide, G2061, which involves the essential keto group of all three compounds, only minor hydrophobic contacts are formed between the pleuromutilin C14 extensions and any ribosomal component, consistent with the PTC tolerance to amino acid diversity. Efficient drug binding mode is attained by a mechanism based on induced-fit motions exploiting the ribosomal intrinsic functional flexibility and resulting in conformational rearrangements that seal the pleuromutilin-binding pocket and tightens it up. Comparative studies identified a network of remote interactions around the PTC, indicating that pleuromutilins selectivity is acquired by nonconserved nucleotides residing in the PTC vicinity, in a fashion resembling allosterism. Likewise, pleuromutilin resistant mechanisms involve nucleotides residing in the environs of the binding pocket, consistent with their slow resistance-development rates.
-===The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080===
+Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity.,Davidovich C, Bashan A, Auerbach-Nevo T, Yaggie RD, Gontarek RR, Yonath A Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4291-6. Epub 2007 Mar 8. PMID:17360517<ref>PMID:17360517</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_17360517}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 2ogn" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 17360517 is the PubMed ID number.
--->
-{{ABSTRACT_PUBMED_17360517}}
-==About this Structure==
-[[2ogn]] is a 1 chain structure of [[Ribosomal protein L3]] and [[Ribosomal protein L6]] with sequence from [http://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OGN OCA].
 ==See Also==
-*[[Ribosomal protein L3]]
+*[[Ribosomal protein L3|Ribosomal protein L3]]
-*[[Ribosomal protein L6]]
+== References ==
+<references/>
-==Reference==
+__TOC__
-<ref group="xtra">PMID:17360517</ref><references group="xtra"/>
+</StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Auerbach-Nevo, T.]]
+[[Category: Large Structures]]
-[[Category: Bashan, A.]]
+[[Category: Auerbach-Nevo T]]
-[[Category: Davidovich, C.]]
+[[Category: Bashan A]]
-[[Category: Yonath, A.]]
+[[Category: Davidovich C]]
-[[Category: Antibiotic]]
+[[Category: Yonath A]]
-[[Category: Peptidyl transferase center]]
-[[Category: Pleuromutilin]]
-[[Category: Ptc]]
-[[Category: Ribosome]]
-[[Category: Sb-280080]]