4zgn - Revision history

OCA at 11:00, 10 January 2024

OCA — Wed, 10 Jan 2024 11:00:03 GMT

←Older revision		Revision as of 11:00, 10 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>		<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [https://pdbe.org/4zgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [https://www.ebi.ac.uk/pdbsum/4zgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zgn 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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [https://pdbe.org/4zgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [https://www.ebi.ac.uk/pdbsum/4zgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zgn ProSAT]</span></td></tr>
	</table>		</table>

OCA at 07:27, 18 May 2023

OCA — Thu, 18 May 2023 07:27:04 GMT

←Older revision		Revision as of 07:27, 18 May 2023
Line 3:		Line 3:
	<StructureSection load='4zgn' size='340' side='right'caption='[[4zgn]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='4zgn' size='340' side='right'caption='[[4zgn]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~] and [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cdc123, SPAP27G11.03 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), GCD11, TIF213, YER025W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [https://pdbe.org/4zgn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [https://www.ebi.ac.uk/pdbsum/4zgn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4zgn 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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [~~http~~://pdbe.org/4zgn PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4zgn PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4zgn ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http://www.uniprot.org/uniprot/CD123_SCHPO CD123_SCHPO]] Regulates the cell cycle in a nutrient dependent manner. [[http~~://www.uniprot.org/uniprot/IF2G_YEAST IF2G_YEAST]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.	+	[https://www.uniprot.org/uniprot/IF2G_YEAST IF2G_YEAST] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 20:

	==See Also==		==See Also==
-	*[[Eukaryotic initiation factor\|Eukaryotic initiation factor]]	+	*[[Eukaryotic initiation factor 3D structures\|Eukaryotic initiation factor 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arnold, L]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Dubiez, E]]	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	[[Category: Mechulam, Y]]	+	[[Category: Arnold L]]
-	[[Category: Panvert, M]]	+	[[Category: Dubiez E]]
-	[[Category: Perez, J]]	+	[[Category: Mechulam Y]]
-	[[Category: Schmitt, E]]	+	[[Category: Panvert M]]
-	[[Category: Seufert, W]]	+	[[Category: Perez J]]
-	~~[[Category: Atp-grasp fold]]~~	+	[[Category: Schmitt E]]
-	~~[[Category: Cell cycle]]~~	+	[[Category: Seufert W]]
-	~~[[Category: Eif2 assembly~~]]	+

OCA at 06:55, 19 June 2019

OCA — Wed, 19 Jun 2019 06:55:31 GMT

←Older revision		Revision as of 06:55, 19 June 2019
Line 1:		Line 1:
		+
	==Structure Cdc123 complexed with the C-terminal domain of eIF2gamma==		==Structure Cdc123 complexed with the C-terminal domain of eIF2gamma==
-	<StructureSection load='4zgn' size='340' side='right' caption='[[4zgn]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='4zgn' size='340' side='right'caption='[[4zgn]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [http://pdbe.org/4zgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [http://www.ebi.ac.uk/pdbsum/4zgn PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cdc123, SPAP27G11.03 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast]), GCD11, TIF213, YER025W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [http://pdbe.org/4zgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [http://www.ebi.ac.uk/pdbsum/4zgn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4zgn ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 4zgn" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4zgn" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Eukaryotic initiation factor\|Eukaryotic initiation factor]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Fission yeast]]
		+	[[Category: Large Structures]]
	[[Category: Arnold, L]]		[[Category: Arnold, L]]
	[[Category: Dubiez, E]]		[[Category: Dubiez, E]]

OCA at 14:35, 30 September 2015

OCA — Wed, 30 Sep 2015 14:35:59 GMT

←Older revision		Revision as of 14:35, 30 September 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Structure Cdc123 complexed with the C-terminal domain of eIF2gamma==
		+	<StructureSection load='4zgn' size='340' side='right' caption='[[4zgn]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4zgn]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ZGN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ZGN FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=4zgn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4zgn OCA], [http://pdbe.org/4zgn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4zgn RCSB], [http://www.ebi.ac.uk/pdbsum/4zgn PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CD123_SCHPO CD123_SCHPO]] Regulates the cell cycle in a nutrient dependent manner. [[http://www.uniprot.org/uniprot/IF2G_YEAST IF2G_YEAST]] eIF-2 functions in the early steps of protein synthesis by forming a ternary complex with GTP and initiator tRNA. This complex binds to a 40S ribosomal subunit, followed by mRNA binding to form a 43S preinitiation complex. Junction of the 60S ribosomal subunit to form the 80S initiation complex is preceded by hydrolysis of the GTP bound to eIF-2 and release of an eIF-2-GDP binary complex. In order for eIF-2 to recycle and catalyze another round of initiation, the GDP bound to eIF-2 must exchange with GTP by way of a reaction catalyzed by eIF-2B.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eukaryotic initiation factor 2 (eIF2), a heterotrimeric guanosine triphosphatase, has a central role in protein biosynthesis by supplying methionylated initiator tRNA to the ribosomal translation initiation complex and by serving as a target for translational control in response to stress. Recent work identified a novel step indispensable for eIF2 function: assembly of eIF2 from its three subunits by the cell proliferation protein Cdc123. We report the first crystal structure of a Cdc123 representative, that from Schizosaccharomyces pombe, both isolated and bound to domain III of Saccharomyces cerevisiae eIF2gamma. The structures show that Cdc123 resembles enzymes of the ATP-grasp family. Indeed, Cdc123 binds ATP-Mg(2+), and conserved residues contacting ATP-Mg(2+) are essential for Cdc123 to support eIF2 assembly and cell viability. A docking of eIF2alphagamma onto Cdc123, combined with genetic and biochemical experiments, allows us to propose a model explaining how Cdc123 participates in the biogenesis of eIF2 through facilitating assembly of eIF2gamma to eIF2alpha.

-	~~The entry 4zgn is ON HOLD~~	+	Cdc123, a Cell Cycle Regulator Needed for eIF2 Assembly, Is an ATP-Grasp Protein with Unique Features.,Panvert M, Dubiez E, Arnold L, Perez J, Mechulam Y, Seufert W, Schmitt E Structure. 2015 Sep 1;23(9):1596-608. doi: 10.1016/j.str.2015.06.014. Epub 2015, Jul 23. PMID:26211610<ref>PMID:26211610</ref>

-	~~Authors: Panvert~~, M.~~, Dubiez, E~~.~~, Arnold, L., Perez, J., Seufert, W., Mechulam, Y., Schmitt, E~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 4zgn" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
-	[[Category: ~~Schmitt~~, E]]	+	<references/>
-	[[Category: ~~Perez~~, J]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Arnold, L]]
		+	[[Category: Dubiez, E]]
	[[Category: Mechulam, Y]]		[[Category: Mechulam, Y]]
-	[[Category: Dubiez, E]]
	[[Category: Panvert, M]]		[[Category: Panvert, M]]
-	[[Category: ~~Arnold~~, L]]	+	[[Category: Perez, J]]
		+	[[Category: Schmitt, E]]
	[[Category: Seufert, W]]		[[Category: Seufert, W]]
		+	[[Category: Atp-grasp fold]]
		+	[[Category: Cell cycle]]
		+	[[Category: Eif2 assembly]]

OCA: Protected "4zgn" [edit=sysop:move=sysop]

OCA — Thu, 30 Apr 2015 10:22:06 GMT

Protected "4zgn" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:22, 30 April 2015

OCA: New page: '''Unreleased structure''' The entry 4zgn is ON HOLD Authors: Panvert, M., Dubiez, E., Arnold, L., Perez, J., Seufert, W., Mechulam, Y., Schmitt, E. Description: [[Category: Unrelease...

OCA — Thu, 30 Apr 2015 10:22:04 GMT

New page: '''Unreleased structure''' The entry 4zgn is ON HOLD Authors: Panvert, M., Dubiez, E., Arnold, L., Perez, J., Seufert, W., Mechulam, Y., Schmitt, E. Description: [[Category: Unrelease...

New page

'''Unreleased structure'''

The entry 4zgn is ON HOLD

Authors: Panvert, M., Dubiez, E., Arnold, L., Perez, J., Seufert, W., Mechulam, Y., Schmitt, E.

Description:
[[Category: Unreleased Structures]]
[[Category: Schmitt, E]]
[[Category: Perez, J]]
[[Category: Mechulam, Y]]
[[Category: Dubiez, E]]
[[Category: Panvert, M]]
[[Category: Arnold, L]]
[[Category: Seufert, W]]