3wy9 - Revision history

OCA at 19:22, 29 May 2024

OCA — Wed, 29 May 2024 19:22:43 GMT

←Older revision		Revision as of 19:22, 29 May 2024
Line 1:		Line 1:

	==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==		==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==
-	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]]' scene=''>	+	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wy9]] 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=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 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]] 2.3Å</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/EF1A_PYRHO EF1A_PYRHO] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In all organisms, the large ribosomal subunit contains multiple copies of a flexible protein, the so-called 'stalk'. The C-terminal domain (CTD) of the stalk interacts directly with the translational GTPase factors, and this interaction is required for factor-dependent activity on the ribosome. Here we have determined the structure of a complex of the CTD of the archaeal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha at 2.3 A resolution. The structure showed that the CTD of aP1 formed a long extended alpha-helix, which bound to a cleft between domains 1 and 3 of aEF1alpha, and bridged these domains. This binding between the CTD of aP1 and the aEF1alphaGDP complex was formed mainly by hydrophobic interactions. The docking analysis showed that the CTD of aP1 can bind to aEF1alphaGDP located on the ribosome. An additional biochemical assay demonstrated that the CTD of aP1 also bound to the aEF1alphaGTPaminoacyl-tRNA complex. These results suggest that the CTD of aP1 interacts with aEF1alpha at various stages in translation. Furthermore, phylogenetic perspectives and functional analyses suggested that the eukaryotic stalk protein also interacts directly with domains 1 and 3 of eEF1alpha, in a manner similar to the interaction of archaeal aP1 with aEF1alpha.
		+
		+	Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1alpha.,Ito K, Honda T, Suzuki T, Miyoshi T, Murakami R, Yao M, Uchiumi T Nucleic Acids Res. 2014 Dec 16;42(22):14042-52. doi: 10.1093/nar/gku1248. Epub, 2014 Nov 26. PMID:25428348<ref>PMID:25428348</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3wy9" 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>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pyrococcus horikoshii OT3]]
	[[Category: Honda T]]		[[Category: Honda T]]
	[[Category: Ito K]]		[[Category: Ito K]]

OCA at 10:37, 31 August 2022

OCA — Wed, 31 Aug 2022 10:37:51 GMT

←Older revision		Revision as of 10:37, 31 August 2022
Line 1:		Line 1:

	==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==		==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==
-	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]]~~, [[Resolution\|resolution]] 2.30Å~~' scene=''>	+	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3wy9]] is a 4 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>
-	</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>~~	+	</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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wya\|3wya]]</div></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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/EF1A_PYRHO EF1A_PYRHO]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[https://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 ==
-	In all organisms, the large ribosomal subunit contains multiple copies of a flexible protein, the so-called 'stalk'. The C-terminal domain (CTD) of the stalk interacts directly with the translational GTPase factors, and this interaction is required for factor-dependent activity on the ribosome. Here we have determined the structure of a complex of the CTD of the archaeal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha at 2.3 A resolution. The structure showed that the CTD of aP1 formed a long extended alpha-helix, which bound to a cleft between domains 1 and 3 of aEF1alpha, and bridged these domains. This binding between the CTD of aP1 and the aEF1alphaGDP complex was formed mainly by hydrophobic interactions. The docking analysis showed that the CTD of aP1 can bind to aEF1alphaGDP located on the ribosome. An additional biochemical assay demonstrated that the CTD of aP1 also bound to the aEF1alphaGTPaminoacyl-tRNA complex. These results suggest that the CTD of aP1 interacts with aEF1alpha at various stages in translation. Furthermore, phylogenetic perspectives and functional analyses suggested that the eukaryotic stalk protein also interacts directly with domains 1 and 3 of eEF1alpha, in a manner similar to the interaction of archaeal aP1 with aEF1alpha.
-
-	Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1alpha.,Ito K, Honda T, Suzuki T, Miyoshi T, Murakami R, Yao M, Uchiumi T Nucleic Acids Res. 2014 Dec 16;42(22):14042-52. doi: 10.1093/nar/gku1248. Epub, 2014 Nov 26. PMID:25428348<ref>PMID:25428348</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3wy9" 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>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Honda, T]]	+	[[Category: Honda T]]
-	[[Category: Ito, K]]	+	[[Category: Ito K]]
-	[[Category: Miyoshi, T]]	+	[[Category: Miyoshi T]]
-	[[Category: Murakami, R]]	+	[[Category: Murakami R]]
-	[[Category: Suzuki, T]]	+	[[Category: Suzuki T]]
-	[[Category: Uchiumi, T]]	+	[[Category: Uchiumi T]]
-	[[Category: Yao, M]]	+	[[Category: Yao M]]
-	~~[[Category: Aminoacyl-trna]]~~	+
-	~~[[Category: Aminoacyl-trna delivery]]~~	+
-	~~[[Category: Gtp]]~~	+
-	~~[[Category: Gtpase]]~~	+
-	~~[[Category: Multi-domain]]~~	+
-	~~[[Category: Stalk protein]]~~	+
-	~~[[Category: Translation-ribosomal protein complex~~]]	+

OCA at 05:00, 25 August 2022

OCA — Thu, 25 Aug 2022 05:00:05 GMT

←Older revision		Revision as of 05:00, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wy9]] is a 4 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wy9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>
	</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>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wya\|3wya]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wya\|3wya]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tuf, PH1484, PHCC033 ([https://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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
	</table>		</table>
Line 28:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]
	[[Category: Honda, T]]		[[Category: Honda, T]]
	[[Category: Ito, K]]		[[Category: Ito, K]]

OCA at 05:35, 10 August 2022

OCA — Wed, 10 Aug 2022 05:35:29 GMT

←Older revision		Revision as of 05:35, 10 August 2022
Line 1:		Line 1:

	==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==		==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==
-	<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='3wy9' size='340' side='right'caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wy9]] 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=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wy9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3WY9 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" id="ligandDat"><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">[[3wya\|3wya]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3wya\|3wya]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tuf, PH1484, PHCC033 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tuf, PH1484, PHCC033 ([https://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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [~~http~~://pdbe.org/3wy9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [https://pdbe.org/3wy9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [https://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/EF1A_PYRHO EF1A_PYRHO]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[~~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/EF1A_PYRHO EF1A_PYRHO]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[https://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Elongation factor\|Elongation factor]]	+	*[[Elongation factor 3D structures\|Elongation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Honda, T]]		[[Category: Honda, T]]

OCA at 09:00, 21 February 2019

OCA — Thu, 21 Feb 2019 09:00:49 GMT

←Older revision		Revision as of 09:00, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3wy9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WY9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3wy9]] 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=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WY9 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">[[3wya\|3wya]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wya\|3wya]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tuf, PH1484, PHCC033 ([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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [http://pdbe.org/3wy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [http://pdbe.org/3wy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
	</table>		</table>
Line 26:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus horikoshii]]
	[[Category: Honda, T]]		[[Category: Honda, T]]
	[[Category: Ito, K]]		[[Category: Ito, K]]

OCA at 05:20, 5 August 2016

OCA — Fri, 05 Aug 2016 05:20:39 GMT

←Older revision		Revision as of 05:20, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==		==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==
	<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
Line 5:		Line 6:
	</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">[[3wya\|3wya]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wya\|3wya]]</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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wy9 PDBsum]</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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [http://pdbe.org/3wy9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wy9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3wy9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3wy9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Elongation factor\|Elongation factor]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:50, 24 December 2014

OCA — Wed, 24 Dec 2014 10:50:46 GMT

←Older revision		Revision as of 10:50, 24 December 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha==
		+	<StructureSection load='3wy9' size='340' side='right' caption='[[3wy9]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3wy9]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3WY9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3WY9 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>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3wya\|3wya]]</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=3wy9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3wy9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3wy9 RCSB], [http://www.ebi.ac.uk/pdbsum/3wy9 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/EF1A_PYRHO EF1A_PYRHO]] This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis.[HAMAP-Rule:MF_00118] [[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 ==
		+	In all organisms, the large ribosomal subunit contains multiple copies of a flexible protein, the so-called 'stalk'. The C-terminal domain (CTD) of the stalk interacts directly with the translational GTPase factors, and this interaction is required for factor-dependent activity on the ribosome. Here we have determined the structure of a complex of the CTD of the archaeal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha at 2.3 A resolution. The structure showed that the CTD of aP1 formed a long extended alpha-helix, which bound to a cleft between domains 1 and 3 of aEF1alpha, and bridged these domains. This binding between the CTD of aP1 and the aEF1alphaGDP complex was formed mainly by hydrophobic interactions. The docking analysis showed that the CTD of aP1 can bind to aEF1alphaGDP located on the ribosome. An additional biochemical assay demonstrated that the CTD of aP1 also bound to the aEF1alphaGTPaminoacyl-tRNA complex. These results suggest that the CTD of aP1 interacts with aEF1alpha at various stages in translation. Furthermore, phylogenetic perspectives and functional analyses suggested that the eukaryotic stalk protein also interacts directly with domains 1 and 3 of eEF1alpha, in a manner similar to the interaction of archaeal aP1 with aEF1alpha.

-	~~The entry 3wy9 is ON HOLD~~	+	Molecular insights into the interaction of the ribosomal stalk protein with elongation factor 1alpha.,Ito K, Honda T, Suzuki T, Miyoshi T, Murakami R, Yao M, Uchiumi T Nucleic Acids Res. 2014 Dec 16;42(22):14042-52. doi: 10.1093/nar/gku1248. Epub, 2014 Nov 26. PMID:25428348<ref>PMID:25428348</ref>

-	~~Authors: Ito~~, K., Honda, T~~., Suzuki, T.~~, Miyoshi, T., Murakami, R~~., Yao, M.~~, Uchiumi, T.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Crystal structure of a complex of the archaeal ribosomal stalk~~ protein ~~aP1 and the GDP~~-~~bound archaeal elongation factor aEF1alpha~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Honda, T]]
		+	[[Category: Ito, K]]
		+	[[Category: Miyoshi, T]]
		+	[[Category: Murakami, R]]
		+	[[Category: Suzuki, T]]
		+	[[Category: Uchiumi, T]]
		+	[[Category: Yao, M]]
		+	[[Category: Aminoacyl-trna]]
		+	[[Category: Aminoacyl-trna delivery]]
		+	[[Category: Gtp]]
		+	[[Category: Gtpase]]
		+	[[Category: Multi-domain]]
		+	[[Category: Stalk protein]]
		+	[[Category: Translation-ribosomal protein complex]]

OCA: Protected "3wy9" [edit=sysop:move=sysop]

OCA — Thu, 04 Sep 2014 03:34:45 GMT

Protected "3wy9" [edit=sysop:move=sysop]

←Older revision

Revision as of 03:34, 4 September 2014

OCA: New page: '''Unreleased structure''' The entry 3wy9 is ON HOLD Authors: Ito, K., Honda, T., Suzuki, T., Miyoshi, T., Murakami, R., Yao, M., Uchiumi, T. Description: Crystal structure of a comple...

OCA — Thu, 04 Sep 2014 03:34:42 GMT

New page: '''Unreleased structure''' The entry 3wy9 is ON HOLD Authors: Ito, K., Honda, T., Suzuki, T., Miyoshi, T., Murakami, R., Yao, M., Uchiumi, T. Description: Crystal structure of a comple...

New page

'''Unreleased structure'''

The entry 3wy9 is ON HOLD

Authors: Ito, K., Honda, T., Suzuki, T., Miyoshi, T., Murakami, R., Yao, M., Uchiumi, T.

Description: Crystal structure of a complex of the archaeal ribosomal stalk protein aP1 and the GDP-bound archaeal elongation factor aEF1alpha