2efe - Revision history

OCA at 13:49, 13 March 2024

2024-03-13T13:49:40Z

← Older revision		Revision as of 13:49, 13 March 2024
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	<StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID~~-~~GUANYLATE+ESTER'>GNH</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]] 2.08Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [https://pdbe.org/2efe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [https://www.ebi.ac.uk/pdbsum/2efe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe 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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [https://pdbe.org/2efe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [https://www.ebi.ac.uk/pdbsum/2efe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> ~~[[https://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>~~		[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2efe ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2efe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7.VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP beta-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP beta-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.

	GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system.,Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S J Biol Chem. 2010 Nov 19;285(47):36689-97. Epub 2010 Sep 10. PMID:20833725<ref>PMID:20833725</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2efe" style="background-color:#fffaf0;"></div>~~
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Arath~~]]		[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ihara, K]]		[[Category: Ihara K]]
	[[Category: Uejima, T]]		[[Category: Uejima T]]
	[[Category: Wakatsuki, S]]		[[Category: Wakatsuki S]]
	~~[[Category: Gef]]~~
	~~[[Category: Gtpase]]~~
	~~[[Category: Nucleotide]]~~
	~~[[Category: Rab5]]~~
	~~[[Category: Transport protein]]~~
	~~[[Category: Vps9~~]]

OCA at 17:23, 15 December 2021

2021-12-15T17:23:52Z

← Older revision		Revision as of 17:23, 15 December 2021
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	<StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</div></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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [~~http~~://pdbe.org/2efe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2efe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe 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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [https://pdbe.org/2efe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [https://www.ebi.ac.uk/pdbsum/2efe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[~~http~~://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>		[[https://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[https://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 08:32, 11 March 2020

2020-03-11T08:32:08Z

← Older revision		Revision as of 08:32, 11 March 2020
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	==Ara7-GDPNH2/AtVps9a==		==Ara7-GDPNH2/AtVps9a==
	<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2efe' size='340' side='right'caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Arath]]		[[Category: Arath]]
			[[Category: Large Structures]]
	[[Category: Ihara, K]]		[[Category: Ihara, K]]
	[[Category: Uejima, T]]		[[Category: Uejima, T]]

OCA at 07:15, 6 June 2018

2018-06-06T07:15:32Z

← Older revision		Revision as of 07:15, 6 June 2018
Line 1:		Line 1:

	==Ara7-GDPNH2/AtVps9a==		==Ara7-GDPNH2/AtVps9a==
	<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://pdbe.org/2efe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe 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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://pdbe.org/2efe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2efe ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efe_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efe_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 05:17, 9 February 2016

2016-02-09T05:17:16Z

← Older revision		Revision as of 05:17, 9 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2efe ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 18:59, 10 September 2015

2015-09-10T18:59:53Z

← Older revision		Revision as of 18:59, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>		<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arabidopsis_thaliana Arabidopsis thaliana~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe 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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://pdbe.org/2efe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/~~Q9LT31_ARATH Q9LT31_ARATH~~]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[http://www.uniprot.org/uniprot/~~Q9SN68_ARATH Q9SN68_ARATH~~]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>		[[http://www.uniprot.org/uniprot/VPS9A_ARATH VPS9A_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[http://www.uniprot.org/uniprot/RAF2B_ARATH RAF2B_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	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 2efe" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Arabidopsis thaliana~~]]		[[Category: Arath]]
	[[Category: Ihara, K]]		[[Category: Ihara, K]]
	[[Category: Uejima, T]]		[[Category: Uejima, T]]

OCA at 04:41, 25 December 2014

2014-12-25T04:41:47Z

← Older revision		Revision as of 04:41, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>		<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe 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=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q9LT31_ARATH Q9LT31_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[http://www.uniprot.org/uniprot/Q9SN68_ARATH Q9SN68_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Ihara, K.]]		[[Category: Ihara, K]]
	[[Category: Uejima, T.]]		[[Category: Uejima, T]]
	[[Category: Wakatsuki, S.]]		[[Category: Wakatsuki, S]]
	[[Category: Gef]]		[[Category: Gef]]
	[[Category: Gtpase]]		[[Category: Gtpase]]

OCA at 10:08, 3 October 2014

2014-10-03T10:08:23Z

← Older revision		Revision as of 10:08, 3 October 2014
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	~~{{STRUCTURE_2efe~~\| ~~PDB~~=2efe \| ~~SCENE~~= }}		==Ara7-GDPNH2/AtVps9a==
	===~~Ara7~~-~~GDPNH2~~/~~AtVps9a~~===		<StructureSection load='2efe' size='340' side='right' caption='[[2efe]], [[Resolution\|resolution]] 2.08Å' scene=''>
	~~{{ABSTRACT_PUBMED_20833725}}~~		== Structural highlights ==
			<table><tr><td colspan='2'>[[2efe]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EFE FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GNH:AMINOPHOSPHONIC+ACID-GUANYLATE+ESTER'>GNH</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2fec\|2fec]], [[2efd\|2efd]], [[2efh\|2efh]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2efe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2efe OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2efe RCSB], [http://www.ebi.ac.uk/pdbsum/2efe PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ef/2efe_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Many GTPases regulate intracellular transport and signaling in eukaryotes. Guanine nucleotide exchange factors (GEFs) activate GTPases by catalyzing the exchange of their GDP for GTP. Here we present crystallographic and biochemical studies of a GEF reaction with four crystal structures of Arabidopsis thaliana ARA7, a plant homolog of Rab5 GTPase, in complex with its GEF, VPS9a, in the nucleotide-free and GDP-bound forms, as well as a complex with aminophosphonic acid-guanylate ester and ARA7.VPS9a(D185N) with GDP. Upon complex formation with ARA7, VPS9 wedges into the interswitch region of ARA7, inhibiting the coordination of Mg(2+) and decreasing the stability of GDP binding. The aspartate finger of VPS9a recognizes GDP beta-phosphate directly and pulls the P-loop lysine of ARA7 away from GDP beta-phosphate toward switch II to further destabilize GDP for its release during the transition from the GDP-bound to nucleotide-free intermediates in the nucleotide exchange reaction.

	~~==Function==~~		GDP-bound and nucleotide-free intermediates of the guanine nucleotide exchange in the Rab5.Vps9 system.,Uejima T, Ihara K, Goh T, Ito E, Sunada M, Ueda T, Nakano A, Wakatsuki S J Biol Chem. 2010 Nov 19;285(47):36689-97. Epub 2010 Sep 10. PMID:20833725<ref>PMID:20833725</ref>
	~~[[http://www.uniprot.org/uniprot/Q9LT31_ARATH Q9LT31_ARATH]] Functions as~~ guanine nucleotide exchange ~~factor (GEF) for Rab small GTPases~~. ~~Activates specifically RABF1~~, ~~RABF2A and RABF2B proteins. Required for early stages of embryogenesis~~, ~~cytokinesis~~, ~~embryogenesis~~, ~~and organ development~~. ~~Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1~~.~~<ref>PMID:18055610</ref> <ref>~~PMID:20833725~~</ref> [[http://www.uniprot.org/uniprot/Q9SN68_ARATH Q9SN68_ARATH]] Endosomal protein that may be involved in endocytosis.~~<ref>PMID:20833725</ref>

	~~==About this Structure==~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	~~[[2efe]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2EFE OCA].~~		</div>
			== References ==
	==~~Reference~~==		<references/>
	~~<ref group="xtra">PMID:020833725</ref>~~<references ~~group="xtra"~~/><~~references~~/>		__TOC__
			</StructureSection>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Ihara, K.]]		[[Category: Ihara, K.]]

OCA at 08:47, 23 April 2014

2014-04-23T08:47:06Z

← Older revision		Revision as of 08:47, 23 April 2014
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	~~[[Image:2efe.png\|left\|200px]]~~

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2efe", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_2efe\| PDB=2efe \| SCENE= }}		{{STRUCTURE_2efe\| PDB=2efe \| SCENE= }}

	===Ara7-GDPNH2/AtVps9a===		===Ara7-GDPNH2/AtVps9a===
			{{ABSTRACT_PUBMED_20833725}}

			==Function==
	~~<!--~~		[[http://www.uniprot.org/uniprot/Q9LT31_ARATH Q9LT31_ARATH]] Functions as guanine nucleotide exchange factor (GEF) for Rab small GTPases. Activates specifically RABF1, RABF2A and RABF2B proteins. Required for early stages of embryogenesis, cytokinesis, embryogenesis, and organ development. Is essential for the establishment or maintenance of the polar localization of the auxin efflux carrier PIN1.<ref>PMID:18055610</ref> <ref>PMID:20833725</ref> [[http://www.uniprot.org/uniprot/Q9SN68_ARATH Q9SN68_ARATH]] Endosomal protein that may be involved in endocytosis.<ref>PMID:20833725</ref>
	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_20833725}}~~, ~~adds~~ the ~~Publication Abstract to~~ the ~~page~~
	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where~~ 20833725 ~~is the PubMed ID number.~~
	-->
	~~{{ABSTRACT_PUBMED_20833725}}~~

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
	<ref group="xtra">PMID:020833725</ref><references group="xtra"/>		<ref group="xtra">PMID:020833725</ref><references group="xtra"/><references/>
	[[Category: Arabidopsis thaliana]]		[[Category: Arabidopsis thaliana]]
	[[Category: Ihara, K.]]		[[Category: Ihara, K.]]

OCA: Protected "2efe" [edit=sysop:move=sysop]

2011-12-28T06:18:44Z

Protected "2efe" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:18, 28 December 2011
(No difference)