5h7k - Revision history

OCA at 09:15, 20 March 2024

OCA — Wed, 20 Mar 2024 09:15:23 GMT

←Older revision		Revision as of 09:15, 20 March 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/EF2_PYRHO EF2_PYRHO]		[https://www.uniprot.org/uniprot/EF2_PYRHO EF2_PYRHO]
-	<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 5h7k" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]		*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:26, 9 August 2023

OCA — Wed, 09 Aug 2023 07:26:20 GMT

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

	==Crystal structure of Elongation factor 2 GDP-form==		==Crystal structure of Elongation factor 2 GDP-form==
-	<StructureSection load='5h7k' size='340' side='right' caption='[[5h7k]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5h7k' size='340' side='right'caption='[[5h7k]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7k]] is a 1 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=5H7K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7k]] is a 1 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=5H7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H7K FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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]] 1.599Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]]~~, [[~~5h7l~~\|~~5h7l~~]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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=5h7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7k OCA], [https://pdbe.org/5h7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h7k RCSB], [https://www.ebi.ac.uk/pdbsum/5h7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7k 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=5h7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7k OCA], [~~http~~://pdbe.org/5h7k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h7k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h7k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7k ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[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 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5h7k" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5h7k" 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~~]]	+

OCA at 06:05, 8 March 2018

OCA — Thu, 08 Mar 2018 06:05:28 GMT

←Older revision		Revision as of 06:05, 8 March 2018
Line 3:		Line 3:
	<StructureSection load='5h7k' size='340' side='right' caption='[[5h7k]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5h7k' size='340' side='right' caption='[[5h7k]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7k]] is a 1 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=5H7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7K FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7l\|5h7l]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7l\|5h7l]]</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=5h7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7k OCA], [http://pdbe.org/5h7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7k RCSB], [http://www.ebi.ac.uk/pdbsum/5h7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7k 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=5h7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7k OCA], [http://pdbe.org/5h7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7k RCSB], [http://www.ebi.ac.uk/pdbsum/5h7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7k ProSAT]</span></td></tr>
	</table>		</table>
		+	<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 5h7k" style="background-color:#fffaf0;"></div>
		+	== 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 07:08:34 GMT

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

-	~~The entry~~ 5h7k is ~~ON HOLD until May 23 2019~~	+	==Crystal structure of Elongation factor 2 GDP-form==
-		+	<StructureSection load='5h7k' size='340' side='right' caption='[[5h7k]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5h7k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7K FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7j\|5h7j]], [[5h7l\|5h7l]]</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=5h7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7k OCA], [http://pdbe.org/5h7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7k RCSB], [http://www.ebi.ac.uk/pdbsum/5h7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7k ProSAT]</span></td></tr>
		+	</table>
		+	__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]]

OCA at 07:08, 27 December 2017

OCA — Wed, 27 Dec 2017 07:08:48 GMT

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

-	The entry 5h7k is ON HOLD until ~~Dec 27 2018~~	+	The entry 5h7k is ON HOLD until May 23 2019

	Authors:		Authors:

OCA at 06:11, 15 November 2017

OCA — Wed, 15 Nov 2017 06:11:46 GMT

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

-	The entry 5h7k is ON HOLD until ~~Paper Publication~~	+	The entry 5h7k is ON HOLD until Dec 27 2018

	Authors:		Authors:

OCA at 10:44, 27 September 2017

OCA — Wed, 27 Sep 2017 10:44:08 GMT

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

-	The entry 5h7k is ON HOLD	+	The entry 5h7k is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5h7k" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 13:50:37 GMT

Protected "5h7k" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:50, 9 December 2016

OCA: New page: '''Unreleased structure''' The entry 5h7k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 09 Dec 2016 13:50:36 GMT

New page: '''Unreleased structure''' The entry 5h7k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5h7k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]