2zjp: Difference between revisions

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-[[Image:2zjp.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2zjp", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
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-{{STRUCTURE_2zjp|  PDB=2zjp  |  SCENE=  }}
-'''Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans'''
+==Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans==
+<StructureSection load='2zjp' size='340' side='right'caption='[[2zjp]], [[Resolution|resolution]] 3.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2zjp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] and [https://en.wikipedia.org/wiki/Streptomyces_actuosus Streptomyces actuosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZJP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZJP 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]] 3.7&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3GL:(2S,4S)-2-AMINO-4-HYDROXY-PENTANEDIOIC+ACID'>3GL</scene>, <scene name='pdbligand=BB9:(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC+ACID'>BB9</scene>, <scene name='pdbligand=DBU:(2Z)-2-AMINOBUT-2-ENOIC+ACID'>DBU</scene>, <scene name='pdbligand=DHA:2-AMINO-ACRYLIC+ACID'>DHA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MH6:3-HYDROXY-2-IMINOPROPANOIC+ACID'>MH6</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene>, <scene name='pdbligand=NO1:4-(HYDROXYMETHYL)-3-METHYL-1H-INDOLE-2-CARBOXYLIC+ACID'>NO1</scene>, <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=2zjp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zjp OCA], [https://pdbe.org/2zjp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zjp RCSB], [https://www.ebi.ac.uk/pdbsum/2zjp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zjp ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RL33_DEIRA RL33_DEIRA] Binds the 23S rRNA and the E site tRNA.[HAMAP-Rule:MF_00294]
+== 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/zj/2zjp_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=2zjp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis.
-==Overview==
+Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.,Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P Mol Cell. 2008 Apr 11;30(1):26-38. PMID:18406324<ref>PMID:18406324</ref>
-The thiopeptide class of antibiotics targets the GTPase-associated center (GAC) of the ribosome to inhibit translation factor function. Using X-ray crystallography, we have determined the binding sites of thiostrepton (Thio), nosiheptide (Nosi), and micrococcin (Micro), on the Deinococcus radiodurans large ribosomal subunit. The thiopeptides, by binding within a cleft located between the ribosomal protein L11 and helices 43 and 44 of the 23S rRNA, overlap with the position of domain V of EF-G, thus explaining how this class of drugs perturbs translation factor binding to the ribosome. The presence of Micro leads to additional density for the C-terminal domain (CTD) of L7, adjacent to and interacting with L11. The results suggest that L11 acts as a molecular switch to control L7 binding and plays a pivotal role in positioning one L7-CTD monomer on the G' subdomain of EF-G to regulate EF-G turnover during protein synthesis.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-ZJP is a [[Protein complex]] structure of sequences 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=2ZJP OCA].
+</div>
+<div class="pdbe-citations 2zjp" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin., Harms JM, Wilson DN, Schluenzen F, Connell SR, Stachelhaus T, Zaborowska Z, Spahn CM, Fucini P, Mol Cell. 2008 Apr 11;30(1):26-38. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18406324 18406324]
+*[[Ribosome 3D structures|Ribosome 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Connell, S R.]]
+[[Category: Streptomyces actuosus]]
-[[Category: Fucini, P.]]
+[[Category: Connell SR]]
-[[Category: Harms, J M.]]
+[[Category: Fucini P]]
-[[Category: Schluenzen, F.]]
+[[Category: Harms JM]]
-[[Category: Spahn, C M.T.]]
+[[Category: Schluenzen F]]
-[[Category: Stachelhaus, T.]]
+[[Category: Spahn CMT]]
-[[Category: Wilson, D N.]]
+[[Category: Stachelhaus T]]
-[[Category: Zaborowska, Z.]]
+[[Category: Wilson DN]]
-[[Category: 50]]
+[[Category: Zaborowska Z]]
-[[Category: Complex]]
-[[Category: L11]]
-[[Category: Metal-binding]]
-[[Category: Methylation]]
-[[Category: Molecular switch]]
-[[Category: Ribonucleoprotein]]
-[[Category: Ribosomal protein]]
-[[Category: Ribosomal subunit]]
-[[Category: Ribosome]]
-[[Category: Rna-binding]]
-[[Category: Rrna-binding]]
-[[Category: Thiopeptide antibiotic]]
-[[Category: Translational regulation]]
-[[Category: Trna-binding]]
-[[Category: Zinc]]
-[[Category: Zinc-finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 18 12:07:36 2008''