2d3o: Difference between revisions

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 ==Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans==
-<StructureSection load='2d3o' size='340' side='right' caption='[[2d3o]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
+<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution|resolution]] 3.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure 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=2D3O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2D3O FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2d3o]] is a 5 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=2D3O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D3O FirstGlance]. <br>
-</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=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.35&#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=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [https://pdbe.org/2d3o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [https://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RL29_DEIRA RL29_DEIRA]] Binds the 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL24_DEIRA RL24_DEIRA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Contacts trigger factor (TF) when it is bound to the ribosome; this contact may expose a hydrophobic crevice in TF (PubMed:16271892).[HAMAP-Rule:MF_01326_B] [[http://www.uniprot.org/uniprot/RL23_DEIRA RL23_DEIRA]] One of the early assembly protein (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Forms the main docking site for trigger factor binding to the ribosome (PubMed:16091460 and PubMed:16271892).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/TIG_DEIRA TIG_DEIRA]] Involved in protein export. Acts as a chaperone by maintaining the newly synthesized protein in an open conformation. Functions as a peptidyl-prolyl cis-trans isomerase (By similarity). Probably changes conformation upon binding to the ribosome (maybe in particular due to interaction with L24, PubMed:16271892), exposing a hydrophobic crevice that is probably important for its chaperone activity (PubMed:16091460 and PubMed:16271892).[HAMAP-Rule:MF_00303]
+[https://www.uniprot.org/uniprot/RL23_DEIRA RL23_DEIRA] One of the early assembly protein (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. Forms the main docking site for trigger factor binding to the ribosome (PubMed:16091460 and PubMed:16271892).[HAMAP-Rule:MF_01369]
 == 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/d3/2d3o_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d3/2d3o_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=2d3o ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-This study presents the X-ray structure of the N-terminal binding domain of the D. radiodurans trigger factor (TF) in complex with the D. radiodurans large ribosomal subunit. At 3.35 A, a complete description of the interactions with ribosomal proteins L23, L29, and 23S rRNA are disclosed, many of which differ from those found previously for a heterologous bacterial-archaeal TF-ribosome complex. The beta hairpin loop of eubacterial L24, which is shorter in archaeal ribosomes, contacts the TF and severely diminishes the molecular cradle proposed to exist between the TF and ribosome. Bound to the ribosome, TF exposes a hydrophobic crevice large enough to accommodate the nascent polypeptide chain. Superimposition of the full-length TF and the signal-recognition particle (SRP) onto the complex shows that simultaneous cohabitation is possible, in agreement with biochemical data, and suggests a model for the interplay of TF, SRP, and the nascent chain during translation.
-The binding mode of the trigger factor on the ribosome: implications for protein folding and SRP interaction.,Schlunzen F, Wilson DN, Tian P, Harms JM, McInnes SJ, Hansen HA, Albrecht R, Buerger J, Wilbanks SM, Fucini P Structure. 2005 Nov;13(11):1685-94. PMID:16271892<ref>PMID:16271892</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 ==See Also==
+*[[Ribosomal protein L23|Ribosomal protein L23]]
 *[[Ribosomal protein L24|Ribosomal protein L24]]
 *[[Ribosomal protein L29|Ribosomal protein L29]]
-== References ==
+*[[Ribosome 3D structures|Ribosome 3D structures]]
-<references/>
 __TOC__
 </StructureSection>
 [[Category: Deinococcus radiodurans]]
-[[Category: Albrecht, R]]
+[[Category: Large Structures]]
-[[Category: Buerger, J]]
+[[Category: Albrecht R]]
-[[Category: Fucini, P]]
+[[Category: Buerger J]]
-[[Category: Hansen, H A]]
+[[Category: Fucini P]]
-[[Category: Harms, J M]]
+[[Category: Hansen HA]]
-[[Category: McInnes, S J]]
+[[Category: Harms JM]]
-[[Category: Schluenzen, F]]
+[[Category: McInnes SJ]]
-[[Category: Tian, P]]
+[[Category: Schluenzen F]]
-[[Category: Wilbanks, S M]]
+[[Category: Tian P]]
-[[Category: Wilson, D N]]
+[[Category: Wilbanks SM]]
-[[Category: Nascent chain]]
+[[Category: Wilson DN]]
-[[Category: Protein folding]]
-[[Category: Ribosome]]
-[[Category: Srp]]
-[[Category: Trigger factor]]