3cf5: Difference between revisions

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-{{Seed}}
-[[Image:3cf5.png|left|200px]]
-<!--
+==Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans==
-The line below this paragraph, containing "STRUCTURE_3cf5", creates the "Structure Box" on the page.
+<StructureSection load='3cf5' size='340' side='right'caption='[[3cf5]], [[Resolution|resolution]] 3.30&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'>[[3cf5]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Deinococcus_radiodurans Deinococcus radiodurans] and [https://en.wikipedia.org/wiki/Streptomyces_azureus Streptomyces azureus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CF5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CF5 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]] 3.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=DCY:D-CYSTEINE'>DCY</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=QUA:8-HYDROXY-4-(1-HYDROXYETHYL)QUINOLINE-2-CARBOXYLIC+ACID'>QUA</scene>, <scene name='pdbligand=TS9:(2S,3S,4R)-2-AMINO-3,4-DIHYDROXY-3-METHYLPENTANOIC+ACID'>TS9</scene></td></tr>
-{{STRUCTURE_3cf5|  PDB=3cf5  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3cf5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cf5 OCA], [https://pdbe.org/3cf5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cf5 RCSB], [https://www.ebi.ac.uk/pdbsum/3cf5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cf5 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/cf/3cf5_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=3cf5 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.
-===Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3cf5" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18406324}}, adds the Publication Abstract to the page
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18406324 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18406324}}
+__TOC__
+</StructureSection>
-==About this Structure==
-CF5 is a 30 chains 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=3CF5 OCA].
-==Reference==
-<ref group="xtra">PMID:18406324</ref><references group="xtra"/>
 [[Category: Deinococcus radiodurans]]
-[[Category: Connell, S R.]]
+[[Category: Large Structures]]
-[[Category: Fucini, P.]]
+[[Category: Streptomyces azureus]]
-[[Category: Harms, J M.]]
+[[Category: Connell SR]]
-[[Category: Schluenzen, F.]]
+[[Category: Fucini P]]
-[[Category: Spahn, C M.T.]]
+[[Category: Harms JM]]
-[[Category: Stachelhaus, T.]]
+[[Category: Schluenzen F]]
-[[Category: Wilson, D N.]]
+[[Category: Spahn CMT]]
-[[Category: Zaborowska, Z.]]
+[[Category: Stachelhaus T]]
-[[Category: 50]]
+[[Category: Wilson DN]]
-[[Category: Complex]]
+[[Category: Zaborowska Z]]
-[[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 Tue Feb 17 13:16:00 2009''