2d3o - Revision history

OCA at 13:46, 13 March 2024

OCA — Wed, 13 Mar 2024 13:46:08 GMT

←Older revision		Revision as of 13:46, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from ~~[https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and~~ [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>	+	<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'>[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>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.35Å</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>		</table>
	== Function ==		== Function ==
-	[[https://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] [[https://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] [[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] [[https://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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		Line 19:
	</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].		</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="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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2d3o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 24:
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
-	~~== References ==~~	+	*[[Ribosome 3D structures\|Ribosome 3D structures]]
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Albrecht, R]]	+	[[Category: Albrecht R]]
-	[[Category: Buerger, J]]	+	[[Category: Buerger J]]
-	[[Category: Fucini, P]]	+	[[Category: Fucini P]]
-	[[Category: Hansen~~, H A~~]]	+	[[Category: Hansen HA]]
-	[[Category: Harms~~, J M~~]]	+	[[Category: Harms JM]]
-	[[Category: McInnes~~, S J~~]]	+	[[Category: McInnes SJ]]
-	[[Category: Schluenzen, F]]	+	[[Category: Schluenzen F]]
-	[[Category: Tian, P]]	+	[[Category: Tian P]]
-	[[Category: Wilbanks~~, S M~~]]	+	[[Category: Wilbanks SM]]
-	[[Category: Wilson~~, D N]]~~	+	[[Category: Wilson DN]]
-	~~[[Category: Nascent chain]]~~	+
-	~~[[Category: Protein folding]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Srp]]~~	+
-	~~[[Category: Trigger factor~~]]	+

OCA at 10:38, 13 April 2022

OCA — Wed, 13 Apr 2022 10:38:03 GMT

←Older revision		Revision as of 10:38, 13 April 2022
Line 3:		Line 3:
	<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [~~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~~://proteopedia.org/fgij/fg.htm?mol=2D3O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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~~://proteopedia.org/fgij/fg.htm?mol=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [~~http~~://pdbe.org/2d3o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>	+	</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>		</table>
	== Function ==		== 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/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] [[https://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] [[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] [[https://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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 14:55, 8 July 2020

OCA — Wed, 08 Jul 2020 14:55:40 GMT

←Older revision		Revision as of 14:55, 8 July 2020
Line 1:		Line 1:

	==Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans==		==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]] 3.35Å' scene=''>	+	<StructureSection load='2d3o' size='340' side='right'caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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://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://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2d3o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d3o OCA], [http://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	[[Category: Micrococcus radiodurans raj et al. 1960]]		[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
		+	[[Category: Large Structures]]
	[[Category: Albrecht, R]]		[[Category: Albrecht, R]]
	[[Category: Buerger, J]]		[[Category: Buerger, J]]

OCA at 06:35, 30 May 2018

OCA — Wed, 30 May 2018 06:35:06 GMT

←Older revision		Revision as of 06:35, 30 May 2018
Line 1:		Line 1:
		+
	==Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans==		==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]] 3.35Å' scene=''>		<StructureSection load='2d3o' size='340' side='right' caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2d3o]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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>
-	</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://pdbe.org/2d3o PDBe], [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='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://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2d3o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 11:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<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>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:23, 11 September 2015

OCA — Fri, 11 Sep 2015 15:23:11 GMT

←Older revision		Revision as of 15:23, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2d3o' size='340' side='right' caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='2d3o' size='340' side='right' caption='[[2d3o]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== 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 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"micrococcus_radiodurans"_raj_et_al._1960 "micrococcus radiodurans" raj et al. 1960] and [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>
-	</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='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://pdbe.org/2d3o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2d3o RCSB], [http://www.ebi.ac.uk/pdbsum/2d3o PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2d3o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
		+	*[[Ribosomal protein L23\|Ribosomal protein L23]]
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
Line 33:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Micrococcus radiodurans raj et al. 1960]]
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Albrecht, R]]		[[Category: Albrecht, R]]

OCA at 18:20, 25 December 2014

OCA — Thu, 25 Dec 2014 18:20:33 GMT

←Older revision		Revision as of 18:20, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== 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 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>
-	</td></tr><tr><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='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>
-	<table>	+	</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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
-	[[Category: Albrecht, R.]]	+	[[Category: Albrecht, R]]
-	[[Category: Buerger, J.]]	+	[[Category: Buerger, J]]
-	[[Category: Fucini, P.]]	+	[[Category: Fucini, P]]
-	[[Category: Hansen, H A.]]	+	[[Category: Hansen, H A]]
-	[[Category: Harms, J M.]]	+	[[Category: Harms, J M]]
-	[[Category: McInnes, S J.]]	+	[[Category: McInnes, S J]]
-	[[Category: Schluenzen, F.]]	+	[[Category: Schluenzen, F]]
-	[[Category: Tian, P.]]	+	[[Category: Tian, P]]
-	[[Category: Wilbanks, S M.]]	+	[[Category: Wilbanks, S M]]
-	[[Category: Wilson, D N~~.]]~~	+	[[Category: Wilson, D N]]
-	~~[[Category: 50~~]]	+
	[[Category: Nascent chain]]		[[Category: Nascent chain]]
	[[Category: Protein folding]]		[[Category: Protein folding]]

OCA at 05:46, 29 September 2014

OCA — Mon, 29 Sep 2014 05:46:45 GMT

←Older revision		Revision as of 05:46, 29 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2d3o.~~png\|left~~\|200px]]	+	==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]] 3.35Å' 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>
		+	</td></tr><tr><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>
		+	<table>
		+	== 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>
		+	<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].
		+	<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.

-	~~{{STRUCTURE_2d3o\| PDB=2d3o \| SCENE= }}~~	+	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>

-	~~===Structure of Ribosome Binding Domain~~ of the ~~Trigger Factor on the 50S ribosomal subunit from D~~. ~~radiodurans===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16271892}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[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].~~	+

	==See Also==		==See Also==
-	*[[Ribosomal protein L23\|Ribosomal protein L23]]
	*[[Ribosomal protein L24\|Ribosomal protein L24]]		*[[Ribosomal protein L24\|Ribosomal protein L24]]
	*[[Ribosomal protein L29\|Ribosomal protein L29]]		*[[Ribosomal protein L29\|Ribosomal protein L29]]
-	*[[Ribosome\|Ribosome]]	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:016271892<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Albrecht, R.]]		[[Category: Albrecht, R.]]

OCA at 19:54, 20 October 2012

OCA — Sat, 20 Oct 2012 19:54:33 GMT

←Older revision		Revision as of 19:54, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[2d3o]] is a 4 chain structure ~~of [[Ribosomal protein L23]], [[Ribosomal protein L24]], [[Ribosomal protein L29]] and [[Ribosome]]~~ 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].	+	[[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].

	==See Also==		==See Also==

OCA: Protected "2d3o" [edit=sysop:move=sysop]

OCA — Fri, 27 Jul 2012 08:52:11 GMT

Protected "2d3o" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:52, 27 July 2012

OCA at 08:52, 27 July 2012

OCA — Fri, 27 Jul 2012 08:52:08 GMT

←Older revision		Revision as of 08:52, 27 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2d3o.png\|left\|200px]]		[[Image:2d3o.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2d3o", 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.
-	-->
	{{STRUCTURE_2d3o\| PDB=2d3o \| SCENE= }}		{{STRUCTURE_2d3o\| PDB=2d3o \| SCENE= }}

	===Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans===		===Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16271892}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16271892 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16271892}}		{{ABSTRACT_PUBMED_16271892}}

	==About this Structure==		==About this Structure==
-	~~2D3O~~ is a ~~5 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=2D3O OCA].	+	[[2d3o]] is a 4 chain structure of [[Ribosomal protein L23]], [[Ribosomal protein L24]], [[Ribosomal protein L29]] and [[Ribosome]] 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].
		+
		+	==See Also==
		+	*[[Ribosomal protein L23\|Ribosomal protein L23]]
		+	*[[Ribosomal protein L24\|Ribosomal protein L24]]
		+	*[[Ribosomal protein L29\|Ribosomal protein L29]]
		+	*[[Ribosome\|Ribosome]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16271892~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016271892</ref><references group="xtra"/>
	[[Category: Deinococcus radiodurans]]		[[Category: Deinococcus radiodurans]]
	[[Category: Albrecht, R.]]		[[Category: Albrecht, R.]]
Line 41:		Line 35:
	[[Category: Srp]]		[[Category: Srp]]
	[[Category: Trigger factor]]		[[Category: Trigger factor]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 02:00:22 2009''