7yzn - Revision history

OCA at 07:54, 1 May 2024

OCA — Wed, 01 May 2024 07:54:56 GMT

←Older revision		Revision as of 07:54, 1 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[7yzn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>		<table><tr><td colspan='2'>[[7yzn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.7Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn 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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IF2P_PYRAB IF2P_PYRAB]] 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_PYRAB IF2P_PYRAB] 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 ==~~	+
-	In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 A resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.	+
-		+
-	Role of aIF5B in archaeal translation initiation.,Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E Nucleic Acids Res. 2022 Jun 24;50(11):6532-6548. doi: 10.1093/nar/gkac490. PMID:35694843<ref>PMID:35694843</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 7yzn" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:53, 7 September 2022

OCA — Wed, 07 Sep 2022 19:53:30 GMT

←Older revision		Revision as of 19:53, 7 September 2022
Line 3:		Line 3:
	<StructureSection load='7yzn' size='340' side='right'caption='[[7yzn]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='7yzn' size='340' side='right'caption='[[7yzn]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7yzn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7yzn]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi_GE5 Pyrococcus abyssi GE5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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;'>[[7yyp\|7yyp]]</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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn 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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/IF2P_PYRAB IF2P_PYRAB]] 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_PYRAB IF2P_PYRAB]] 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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bourgeois, G]]	+	[[Category: Pyrococcus abyssi GE5]]
-	[[Category: Coureux~~, P D~~]]	+	[[Category: Bourgeois G]]
-	[[Category: Kazan, R]]	+	[[Category: Coureux PD]]
-	[[Category: Mechulam, Y]]	+	[[Category: Kazan R]]
-	[[Category: Schmitt, E]]	+	[[Category: Mechulam Y]]
-	~~[[Category: Eif5b]]~~	+	[[Category: Schmitt E]]
-	~~[[Category: If2]]~~	+
-	~~[[Category: Initiation factor]]~~	+
-	~~[[Category: Initiator trna]]~~	+
-	~~[[Category: Ribosome]]~~	+
-	~~[[Category: Translation~~]]	+

OCA at 06:45, 31 August 2022

OCA — Wed, 31 Aug 2022 06:45:24 GMT

←Older revision		Revision as of 06:45, 31 August 2022
Line 1:		Line 1:

-	==~~n/a~~==	+	==Structure of C-terminally truncated aIF5B from Pyrococcus abyssi complexed with GTP==
-	<StructureSection load='7yzn' size='340' side='right'caption='[[7yzn]]' scene=''>	+	<StructureSection load='7yzn' size='340' side='right'caption='[[7yzn]], [[Resolution\|resolution]] 1.70Å' 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=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7yzn]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN 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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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;'>[[7yyp\|7yyp]]</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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/IF2P_PYRAB IF2P_PYRAB]] 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 ==
		+	In eukaryotes and in archaea late steps of translation initiation involve the two initiation factors e/aIF5B and e/aIF1A. In eukaryotes, the role of eIF5B in ribosomal subunit joining is established and structural data showing eIF5B bound to the full ribosome were obtained. To achieve its function, eIF5B collaborates with eIF1A. However, structural data illustrating how these two factors interact on the small ribosomal subunit have long been awaited. The role of the archaeal counterparts, aIF5B and aIF1A, remains to be extensively addressed. Here, we study the late steps of Pyrococcus abyssi translation initiation. Using in vitro reconstituted initiation complexes and light scattering, we show that aIF5B bound to GTP accelerates subunit joining without the need for GTP hydrolysis. We report the crystallographic structures of aIF5B bound to GDP and GTP and analyze domain movements associated to these two nucleotide states. Finally, we present the cryo-EM structure of an initiation complex containing 30S bound to mRNA, Met-tRNAiMet, aIF5B and aIF1A at 2.7 A resolution. Structural data shows how archaeal 5B and 1A factors cooperate to induce a conformation of the initiator tRNA favorable to subunit joining. Archaeal and eukaryotic features of late steps of translation initiation are discussed.
		+
		+	Role of aIF5B in archaeal translation initiation.,Kazan R, Bourgeois G, Lazennec-Schurdevin C, Larquet E, Mechulam Y, Coureux PD, Schmitt E Nucleic Acids Res. 2022 Jun 24;50(11):6532-6548. doi: 10.1093/nar/gkac490. PMID:35694843<ref>PMID:35694843</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7yzn" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~N/a~~]]	+	[[Category: Bourgeois, G]]
		+	[[Category: Coureux, P D]]
		+	[[Category: Kazan, R]]
		+	[[Category: Mechulam, Y]]
		+	[[Category: Schmitt, E]]
		+	[[Category: Eif5b]]
		+	[[Category: If2]]
		+	[[Category: Initiation factor]]
		+	[[Category: Initiator trna]]
		+	[[Category: Ribosome]]
		+	[[Category: Translation]]

OCA at 07:29, 29 June 2022

OCA — Wed, 29 Jun 2022 07:29:25 GMT

←Older revision		Revision as of 07:29, 29 June 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7yzn ~~is ON HOLD until Paper Publication~~	+	==n/a==
-		+	<StructureSection load='7yzn' size='340' side='right'caption='[[7yzn]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7YZN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7YZN FirstGlance]. <br>
-	~~Description~~:	+	</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=7yzn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7yzn OCA], [https://pdbe.org/7yzn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7yzn RCSB], [https://www.ebi.ac.uk/pdbsum/7yzn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7yzn ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: N/a]]

OCA: Protected "7yzn" [edit=sysop:move=sysop]

OCA — Wed, 02 Mar 2022 05:20:30 GMT

Protected "7yzn" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:20, 2 March 2022

OCA: New page: '''Unreleased structure''' The entry 7yzn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 02 Mar 2022 05:20:29 GMT

New page: '''Unreleased structure''' The entry 7yzn is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7yzn is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]