5h7l - Revision history

OCA at 07:26, 9 August 2023

OCA — Wed, 09 Aug 2023 07:26:22 GMT

←Older revision		Revision as of 07:26, 9 August 2023
Line 1:		Line 1:

	==Complex of Elongation factor 2-50S ribosomal protein L12==		==Complex of Elongation factor 2-50S ribosomal protein L12==
-	<StructureSection load='5h7l' size='340' side='right' caption='[[5h7l]], [[Resolution\|resolution]] 3.10Å' scene=''>	+	<StructureSection load='5h7l' size='340' side='right'caption='[[5h7l]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7l]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H7L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7l]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H7L FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></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]] 3.1Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]]~~, [[~~5h7k~~\|~~5h7k~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~fusA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=70601 Pyrococcus horikoshii])~~</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=5h7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7l OCA], [https://pdbe.org/5h7l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h7l RCSB], [https://www.ebi.ac.uk/pdbsum/5h7l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7l ProSAT]</span></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=5h7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7l OCA], [~~http~~://pdbe.org/5h7l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h7l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h7l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7l ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~RL12_PYRHO RL12_PYRHO~~]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>	+	[https://www.uniprot.org/uniprot/EF2_PYRHO EF2_PYRHO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5h7l" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5h7l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Large Structures]]
-	[[Category: Kato, K]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Tanzawa, T]]	+	[[Category: Kato K]]
-	[[Category: Uchiumi, T]]	+	[[Category: Tanzawa T]]
-	[[Category: Yao, M]]	+	[[Category: Uchiumi T]]
-	~~[[Category: Elongation factor]]~~	+	[[Category: Yao M]]
-	~~[[Category: Gtp-binding]]~~	+
-	~~[[Category: Protein biosynthesis]]~~	+
-	~~[[Category: Translation-ribosomal protein complex~~]]	+

OCA at 06:05, 8 March 2018

OCA — Thu, 08 Mar 2018 06:05:29 GMT

←Older revision		Revision as of 06:05, 8 March 2018
Line 3:		Line 3:
	<StructureSection load='5h7l' size='340' side='right' caption='[[5h7l]], [[Resolution\|resolution]] 3.10Å' scene=''>		<StructureSection load='5h7l' size='340' side='right' caption='[[5h7l]], [[Resolution\|resolution]] 3.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7l]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7l]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7k\|5h7k]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7k\|5h7k]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fusA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</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=5h7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7l OCA], [http://pdbe.org/5h7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7l RCSB], [http://www.ebi.ac.uk/pdbsum/5h7l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7l ProSAT]</span></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=5h7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7l OCA], [http://pdbe.org/5h7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7l RCSB], [http://www.ebi.ac.uk/pdbsum/5h7l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RL12_PYRHO RL12_PYRHO]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>		[[http://www.uniprot.org/uniprot/RL12_PYRHO RL12_PYRHO]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Archaea and eukaryotes have ribosomal P stalks composed of anchor protein P0 and aP1 homodimers (archaea) or P1*P2 heterodimers (eukaryotes). These P stalks recruit translational GTPases to the GTPase-associated center in ribosomes to provide energy during translation. The C-terminus of the P stalk is known to selectively recognize GTPases. Here we investigated the interaction between the P stalk and elongation factor 2 by determining the structures of Pyrococcus horikoshii EF-2 (PhoEF-2) in the Apo-form, GDP-form, GMPPCP-form (GTP-form), and GMPPCP-form bound with 11 C-terminal residues of P1 (P1C11). Helical structured P1C11 binds to a hydrophobic groove between domain G and subdomain G' of PhoEF-2, where is completely different from that of aEF-1alpha in terms of both position and sequence, implying that such interaction characteristic may be requested by how GTPases perform their functions on the ribosome. Combining PhoEF-2 P1-binding assays with a structural comparison of current PhoEF-2 structures and molecular dynamics model of a P1C11-bound GDP form, the conformational changes of the P1C11-binding groove in each form suggest that in response to the translation process, the groove has three states: closed, open, and release for recruiting and releasing GTPases.
		+
		+	The C-terminal helix of ribosomal P stalk recognizes a hydrophobic groove of elongation factor 2 in a novel fashion.,Tanzawa T, Kato K, Girodat D, Ose T, Kumakura Y, Wieden HJ, Uchiumi T, Tanaka I, Yao M Nucleic Acids Res. 2018 Feb 20. pii: 4877024. doi: 10.1093/nar/gky115. PMID:29471537<ref>PMID:29471537</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5h7l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Kato, K]]		[[Category: Kato, K]]
	[[Category: Tanzawa, T]]		[[Category: Tanzawa, T]]

OCA at 07:08, 22 February 2018

OCA — Thu, 22 Feb 2018 07:08:37 GMT

←Older revision		Revision as of 07:08, 22 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5h7l is ~~ON HOLD~~ ~~until May 23 2019~~	+	==Complex of Elongation factor 2-50S ribosomal protein L12==
-		+	<StructureSection load='5h7l' size='340' side='right' caption='[[5h7l]], [[Resolution\|resolution]] 3.10Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5h7l]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7L FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GCP:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>GCP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7k\|5h7k]]</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=5h7l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7l OCA], [http://pdbe.org/5h7l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7l RCSB], [http://www.ebi.ac.uk/pdbsum/5h7l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7l ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RL12_PYRHO RL12_PYRHO]] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. The stalk complex of P.horikoshii binds to E.coli large subunits and confers on them the ability to interact with eukaryotic elongation factors. Each succesive L12 dimer bound along the P0 spine increases the GTPase activity of elongation factors and increases translation by reconsituted ribosomes.<ref>PMID:17804412</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kato, K]]
		+	[[Category: Tanzawa, T]]
		+	[[Category: Uchiumi, T]]
		+	[[Category: Yao, M]]
		+	[[Category: Elongation factor]]
		+	[[Category: Gtp-binding]]
		+	[[Category: Protein biosynthesis]]
		+	[[Category: Translation-ribosomal protein complex]]

OCA at 07:08, 27 December 2017

OCA — Wed, 27 Dec 2017 07:08:51 GMT

←Older revision		Revision as of 07:08, 27 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h7l is ON HOLD until ~~Dec 27 2018~~	+	The entry 5h7l is ON HOLD until May 23 2019

	Authors:		Authors:

OCA at 06:11, 15 November 2017

OCA — Wed, 15 Nov 2017 06:11:49 GMT

←Older revision		Revision as of 06:11, 15 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h7l is ON HOLD until ~~Paper Publication~~	+	The entry 5h7l is ON HOLD until Dec 27 2018

	Authors:		Authors:

OCA at 10:44, 27 September 2017

OCA — Wed, 27 Sep 2017 10:44:11 GMT

←Older revision		Revision as of 10:44, 27 September 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5h7l is ON HOLD	+	The entry 5h7l is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5h7l" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 13:50:40 GMT

Protected "5h7l" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:50, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5h7l is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 13:50:39 GMT

New page: '''Unreleased structure''' The entry 5h7l is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5h7l is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]