5yt0 - Revision history

OCA at 10:24, 27 March 2024

2024-03-27T10:24:59Z

←Older revision		Revision as of 10:24, 27 March 2024
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	==Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B==		==Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B==
-	<StructureSection load='5yt0' size='340' side='right' caption='[[5yt0]], [[Resolution\|resolution]] 1.89Å' scene=''>	+	<StructureSection load='5yt0' size='340' side='right'caption='[[5yt0]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yt0]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Aerpe Aerpe~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YT0 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yt0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aeropyrum_pernix_K1 Aeropyrum pernix K1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YT0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YT0 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]] 1.89Å</td></tr>
-	~~<tr~~ id~~='related'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Related_structure~~\|~~Related:]]</b></td><td class="sblockDat">[[5fg3\|5fg3~~]]</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">~~infB, APE_2374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=5~~&id=272557 AERPE])~~</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=5yt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt0 OCA], [https://pdbe.org/5yt0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yt0 RCSB], [https://www.ebi.ac.uk/pdbsum/5yt0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt0 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=5yt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt0 OCA], [~~http~~://pdbe.org/5yt0 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yt0 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yt0 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt0 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/IF2P_AERPE IF2P_AERPE]] Function in general translation initiation by promoting the binding of the formylmethionine-tRNA to ribosomes. Seems to function along with eIF-2 (By similarity).	+	[https://www.uniprot.org/uniprot/IF2P_AERPE IF2P_AERPE] Function in general translation initiation by promoting the binding of the formylmethionine-tRNA to ribosomes. Seems to function along with eIF-2 (By similarity).
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Ribosomal stalk proteins recruit translation elongation GTPases to the factor-binding center of the ribosome. Initiation factor 5B (eIF5B in eukaryotes and aIF5B in archaea) is a universally conserved GTPase that promotes the joining of the large and small ribosomal subunits during translation initiation. Here we show that aIF5B binds to the C-terminal tail of the stalk protein. In the co-crystal structure, the interaction occurs between the hydrophobic amino acids of the stalk C-terminal tail and a small hydrophobic pocket on the surface of the GTP-binding domain (domain I) of aIF5B. A substitution mutation altering the hydrophobic pocket of yeast eIF5B resulted in a marked reduction in ribosome-dependent eIF5B GTPase activity in vitro In yeast cells, the eIF5B mutation affected growth, and impaired GCN4 expression during amino acid starvation via a defect in start site selection for the first upstream open reading frame in GCN4 mRNA, as observed with eIF5B deletion mutant. Deletion of two of the four stalk proteins diminished poly-ribosome levels (indicating defective translation initiation) and starvation-induced GCN4 expression, both of which were suppressible by eIF5B overexpression. Thus, the mutual interaction between a/eIF5B and the ribosomal stalk plays an important role in subunit joining during translation initiation in vivo.	+
-		+
-	The interaction between the ribosomal stalk proteins and translation initiation factor 5B promotes translation initiation.,Murakami R, Singh CR, Morris J, Tang L, Harmon I, Azuma T, Miyoshi T, Ito K, Asano K, Uchiumi T Mol Cell Biol. 2018 May 29. pii: MCB.00067-18. doi: 10.1128/MCB.00067-18. PMID:29844065<ref>PMID:29844065</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yt0" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Aerpe~~]]	+	[[Category: Aeropyrum pernix K1]]
-	[[Category: Asano, K]]	+	[[Category: Large Structures]]
-	[[Category: Harmon, I]]	+	[[Category: Asano K]]
-	[[Category: Ito, K]]	+	[[Category: Harmon I]]
-	[[Category: Miyoshi, T]]	+	[[Category: Ito K]]
-	[[Category: Morris, J]]	+	[[Category: Miyoshi T]]
-	[[Category: Murakami, R]]	+	[[Category: Morris J]]
-	[[Category: Singh~~, C R~~]]	+	[[Category: Murakami R]]
-	[[Category: Tang, L]]	+	[[Category: Singh CR]]
-	[[Category: Uchiumi, T]]	+	[[Category: Tang L]]
-	~~[[Category: Complex]]~~	+	[[Category: Uchiumi T]]
-	~~[[Category: Ribosomal stalk protein]]~~	+
-	~~[[Category: Translation]]~~	+
-	~~[[Category: Translation initiation factor~~]]	+

OCA at 16:35, 15 August 2018

2018-08-15T16:35:37Z

←Older revision		Revision as of 16:35, 15 August 2018
Line 3:		Line 3:
	<StructureSection load='5yt0' size='340' side='right' caption='[[5yt0]], [[Resolution\|resolution]] 1.89Å' scene=''>		<StructureSection load='5yt0' size='340' side='right' caption='[[5yt0]], [[Resolution\|resolution]] 1.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YT0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yt0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpe Aerpe]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YT0 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">[[5fg3\|5fg3]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5fg3\|5fg3]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">infB, APE_2374 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=272557 AERPE])</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=5yt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt0 OCA], [http://pdbe.org/5yt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt0 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=5yt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt0 OCA], [http://pdbe.org/5yt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt0 ProSAT]</span></td></tr>
	</table>		</table>
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aerpe]]
	[[Category: Asano, K]]		[[Category: Asano, K]]
	[[Category: Harmon, I]]		[[Category: Harmon, I]]

OCA at 05:31, 27 June 2018

2018-06-27T05:31:54Z

←Older revision		Revision as of 05:31, 27 June 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yt0 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the complex of archaeal ribosomal stalk protein aP1 and archaeal translation initiation factor aIF5B==
		+	<StructureSection load='5yt0' size='340' side='right' caption='[[5yt0]], [[Resolution\|resolution]] 1.89Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yt0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YT0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YT0 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">[[5fg3\|5fg3]]</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=5yt0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yt0 OCA], [http://pdbe.org/5yt0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yt0 RCSB], [http://www.ebi.ac.uk/pdbsum/5yt0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yt0 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/IF2P_AERPE IF2P_AERPE]] Function in general translation initiation by promoting the binding of the formylmethionine-tRNA to ribosomes. Seems to function along with eIF-2 (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Ribosomal stalk proteins recruit translation elongation GTPases to the factor-binding center of the ribosome. Initiation factor 5B (eIF5B in eukaryotes and aIF5B in archaea) is a universally conserved GTPase that promotes the joining of the large and small ribosomal subunits during translation initiation. Here we show that aIF5B binds to the C-terminal tail of the stalk protein. In the co-crystal structure, the interaction occurs between the hydrophobic amino acids of the stalk C-terminal tail and a small hydrophobic pocket on the surface of the GTP-binding domain (domain I) of aIF5B. A substitution mutation altering the hydrophobic pocket of yeast eIF5B resulted in a marked reduction in ribosome-dependent eIF5B GTPase activity in vitro In yeast cells, the eIF5B mutation affected growth, and impaired GCN4 expression during amino acid starvation via a defect in start site selection for the first upstream open reading frame in GCN4 mRNA, as observed with eIF5B deletion mutant. Deletion of two of the four stalk proteins diminished poly-ribosome levels (indicating defective translation initiation) and starvation-induced GCN4 expression, both of which were suppressible by eIF5B overexpression. Thus, the mutual interaction between a/eIF5B and the ribosomal stalk plays an important role in subunit joining during translation initiation in vivo.

-	~~Authors~~:	+	The interaction between the ribosomal stalk proteins and translation initiation factor 5B promotes translation initiation.,Murakami R, Singh CR, Morris J, Tang L, Harmon I, Azuma T, Miyoshi T, Ito K, Asano K, Uchiumi T Mol Cell Biol. 2018 May 29. pii: MCB.00067-18. doi: 10.1128/MCB.00067-18. PMID:29844065<ref>PMID:29844065</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yt0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Asano, K]]
		+	[[Category: Harmon, I]]
		+	[[Category: Ito, K]]
		+	[[Category: Miyoshi, T]]
		+	[[Category: Morris, J]]
		+	[[Category: Murakami, R]]
		+	[[Category: Singh, C R]]
		+	[[Category: Tang, L]]
		+	[[Category: Uchiumi, T]]
		+	[[Category: Complex]]
		+	[[Category: Ribosomal stalk protein]]
		+	[[Category: Translation]]
		+	[[Category: Translation initiation factor]]

OCA at 04:56, 29 November 2017

2017-11-29T04:56:57Z

←Older revision		Revision as of 04:56, 29 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yt0 is ON HOLD	+	The entry 5yt0 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5yt0" [edit=sysop:move=sysop]

2017-11-22T06:28:54Z

Protected "5yt0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:28, 22 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yt0 is ON HOLD Authors: Description: Category: Unreleased Structures

2017-11-22T06:28:53Z

New page: '''Unreleased structure''' The entry 5yt0 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yt0 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]