2dym - Revision history

OCA at 13:48, 13 March 2024

2024-03-13T13:48:32Z

←Older revision		Revision as of 13:48, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2dym' size='340' side='right'caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2dym' size='340' side='right'caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYM FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[2dyo\|2dyo]]</div></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]] 2.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">ATG5 ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=4932 ATCC 18824]), ATG16 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])~~</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [https://pdbe.org/2dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [https://www.ebi.ac.uk/pdbsum/2dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym 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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [https://pdbe.org/2dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [https://www.ebi.ac.uk/pdbsum/2dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST]] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref> [[https://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</ref>	+	[https://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 19:
	</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=2dym 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=2dym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the Atg12-Atg5 conjugate further forms a complex with the multimeric protein Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in autophagy, the bulk degradation system conserved in all eukaryotes. We have reported here the crystal structure of Atg5 complexed with the N-terminal region of Atg16 at 1.97A resolution. Atg5 comprises two ubiquitin-like domains that flank a helix-rich domain. The N-terminal region of Atg16 has a helical structure and is bound to the groove formed by these three domains. In vitro analysis showed that Arg-35 and Phe-46 of Atg16 are crucial for the interaction. Atg16, with a mutation at these residues, failed to localize to the pre-autophagosomal structure and could not restore autophagy in Atg16-deficient yeast strains. Furthermore, these Atg16 mutants could not restore a severe reduction in the formation of the Atg8-phosphatidylethanolamine conjugate, another essential factor for autophagy, in Atg16-deficient strains under starvation conditions. These results taken together suggest that the direct interaction between Atg5 and Atg16 is crucial to the performance of their roles in autophagy.
-
-	Structure of Atg5.Atg16, a complex essential for autophagy.,Matsushita M, Suzuki NN, Obara K, Fujioka Y, Ohsumi Y, Inagaki F J Biol Chem. 2007 Mar 2;282(9):6763-72. Epub 2006 Dec 27. PMID:17192262<ref>PMID:17192262</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2dym" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Inagaki, F~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Matsushita, M~~]]	+	[[Category: Inagaki F]]
-	[[Category: ~~Suzuki, N N~~]]	+	[[Category: Matsushita M]]
-	[[Category: ~~Herix-bundle]]~~	+	[[Category: Suzuki NN]]
-	~~[[Category: Protein turnover-protein turnover complex]]~~	+
-	~~[[Category: Ubiquitin-fold~~]]	+

OCA at 11:41, 10 February 2021

2021-02-10T11:41:43Z

←Older revision		Revision as of 11:41, 10 February 2021
Line 1:		Line 1:

	==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==		==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==
-	<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='2dym' size='340' side='right'caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DYM FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dyo\|2dyo]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ATG16 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ATG16 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [~~http~~://pdbe.org/2dym PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dym PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym 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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [https://pdbe.org/2dym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [https://www.ebi.ac.uk/pdbsum/2dym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST]] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref> [[~~http~~://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</ref>	+	[[https://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST]] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref> [[https://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:

	==See Also==		==See Also==
-	*[[Autophagy-related protein\|Autophagy-related protein]]	+	*[[Autophagy-related protein 3D structures\|Autophagy-related protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
		+	[[Category: Large Structures]]
	[[Category: Inagaki, F]]		[[Category: Inagaki, F]]
	[[Category: Matsushita, M]]		[[Category: Matsushita, M]]

OCA at 06:54, 6 June 2018

2018-06-06T06:54:40Z

←Older revision		Revision as of 06:54, 6 June 2018
Line 1:		Line 1:
		+
	==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==		==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==
	<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://pdbe.org/2dym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym 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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://pdbe.org/2dym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dym ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dym_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dy/2dym_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 04:55, 7 February 2016

2016-02-07T04:55:16Z

←Older revision		Revision as of 04:55, 7 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=2dym ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:02, 9 September 2015

2015-09-09T22:02:51Z

←Older revision		Revision as of 22:02, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DYM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym 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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://pdbe.org/2dym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	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 2dym" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Autophagy-related protein\|Autophagy-related protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Saccharomyces cerevisiae~~]]	+	[[Category: Atcc 18824]]
	[[Category: Inagaki, F]]		[[Category: Inagaki, F]]
	[[Category: Matsushita, M]]		[[Category: Matsushita, M]]

OCA at 08:00, 24 December 2014

2014-12-24T08:00:37Z

←Older revision		Revision as of 08:00, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DYM FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DYM FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym 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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATG5_YEAST ATG5_YEAST]] Involved in cytoplasm to vacuole transport (Cvt) and autophagy vesicles formation. Required for ATG8 association to the vesicle membranes.<ref>PMID:8921905</ref> <ref>PMID:8224160</ref> <ref>PMID:9759731</ref> <ref>PMID:10406794</ref> <ref>PMID:10712513</ref> <ref>PMID:11149920</ref> [[http://www.uniprot.org/uniprot/ATG16_YEAST ATG16_YEAST]] Stabilizes the ATG5-ATG12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. Required for ATG8 localization to the pre-autophagosomal structure.<ref>PMID:8224160</ref> <ref>PMID:8663607</ref> <ref>PMID:10406794</ref> <ref>PMID:11689437</ref> <ref>PMID:11897782</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: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Inagaki, F.]]	+	[[Category: Inagaki, F]]
-	[[Category: Matsushita, M.]]	+	[[Category: Matsushita, M]]
-	[[Category: Suzuki, N N.]]	+	[[Category: Suzuki, N N]]
	[[Category: Herix-bundle]]		[[Category: Herix-bundle]]
	[[Category: Protein turnover-protein turnover complex]]		[[Category: Protein turnover-protein turnover complex]]
	[[Category: Ubiquitin-fold]]		[[Category: Ubiquitin-fold]]

OCA at 01:05, 30 September 2014

2014-09-30T01:05:50Z

←Older revision		Revision as of 01:05, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2dym.~~png~~\|~~left~~\|200px]]	+	==The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex==
		+	<StructureSection load='2dym' size='340' side='right' caption='[[2dym]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DYM FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dyo\|2dyo]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae]), ATG16 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=2dym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dym OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dym RCSB], [http://www.ebi.ac.uk/pdbsum/2dym 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/dy/2dym_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 ==
		+	Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the Atg12-Atg5 conjugate further forms a complex with the multimeric protein Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in autophagy, the bulk degradation system conserved in all eukaryotes. We have reported here the crystal structure of Atg5 complexed with the N-terminal region of Atg16 at 1.97A resolution. Atg5 comprises two ubiquitin-like domains that flank a helix-rich domain. The N-terminal region of Atg16 has a helical structure and is bound to the groove formed by these three domains. In vitro analysis showed that Arg-35 and Phe-46 of Atg16 are crucial for the interaction. Atg16, with a mutation at these residues, failed to localize to the pre-autophagosomal structure and could not restore autophagy in Atg16-deficient yeast strains. Furthermore, these Atg16 mutants could not restore a severe reduction in the formation of the Atg8-phosphatidylethanolamine conjugate, another essential factor for autophagy, in Atg16-deficient strains under starvation conditions. These results taken together suggest that the direct interaction between Atg5 and Atg16 is crucial to the performance of their roles in autophagy.

-	~~{{STRUCTURE_2dym\| PDB=2dym \| SCENE= }}~~	+	Structure of Atg5.Atg16, a complex essential for autophagy.,Matsushita M, Suzuki NN, Obara K, Fujioka Y, Ohsumi Y, Inagaki F J Biol Chem. 2007 Mar 2;282(9):6763-72. Epub 2006 Dec 27. PMID:17192262<ref>PMID:17192262</ref>

-	~~===The crystal structure~~ of ~~Saccharomyces cerevisiae Atg5- Atg16(1-46) complex===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17192262}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dym]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017192262<~~/~~ref~~><~~ref group="xtra">PMID:017012802</ref><references group="xtra"~~/>	+
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Inagaki, F.]]		[[Category: Inagaki, F.]]

OCA at 12:11, 23 January 2013

2013-01-23T12:11:35Z

←Older revision		Revision as of 12:11, 23 January 2013
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	[[Image:2dym.png\|left\|200px]]		[[Image:2dym.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dym", 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_2dym\| PDB=2dym \| SCENE= }}		{{STRUCTURE_2dym\| PDB=2dym \| SCENE= }}

	===The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex===		===The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17192262}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17192262 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17192262}}		{{ABSTRACT_PUBMED_17192262}}

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	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17192262~~</ref><ref group="xtra">PMID:~~17012802~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017192262</ref><ref group="xtra">PMID:017012802</ref><references group="xtra"/>
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
	[[Category: Inagaki, F.]]		[[Category: Inagaki, F.]]
Line 28:		Line 17:
	[[Category: Suzuki, N N.]]		[[Category: Suzuki, N N.]]
	[[Category: Herix-bundle]]		[[Category: Herix-bundle]]
-	[[Category: Protein turnover/protein turnover complex]]	+	[[Category: Protein turnover-protein turnover complex]]
	[[Category: Ubiquitin-fold]]		[[Category: Ubiquitin-fold]]

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

2011-03-14T20:27:00Z

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

←Older revision

Revision as of 20:27, 14 March 2011

OCA at 20:26, 14 March 2011

2011-03-14T20:26:58Z

←Older revision		Revision as of 20:26, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2dym.png\|left\|200px]]		[[Image:2dym.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~2DYM~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA].	+	[[2dym]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DYM OCA].

	==Reference==		==Reference==
Line 29:		Line 28:
	[[Category: Suzuki, N N.]]		[[Category: Suzuki, N N.]]
	[[Category: Herix-bundle]]		[[Category: Herix-bundle]]
		+	[[Category: Protein turnover/protein turnover complex]]
	[[Category: Ubiquitin-fold]]		[[Category: Ubiquitin-fold]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:27:53 2009''