6kbm - Revision history

OCA at 10:29, 22 November 2023

OCA — Wed, 22 Nov 2023 10:29:23 GMT

←Older revision		Revision as of 10:29, 22 November 2023
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	<StructureSection load='6kbm' size='340' side='right'caption='[[6kbm]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6kbm' size='340' side='right'caption='[[6kbm]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kbm]] is a 2 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=6KBM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kbm]] is a 2 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=6KBM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KBM FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6kbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbm OCA], [~~http~~://pdbe.org/6kbm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kbm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kbm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbm ProSAT]</span></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]] 2.902Å</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=6kbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbm OCA], [https://pdbe.org/6kbm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kbm RCSB], [https://www.ebi.ac.uk/pdbsum/6kbm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST]] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref> [[http://www.uniprot.org/uniprot/ATG13_YEAST ATG13_YEAST]] Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy. Required for autophosphorylation of ATG1 at 'Thr-226' and its dimerization. May also be involved in the regulation of autophagy through SNF1. Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure. Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation. Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage during stationary phase.<ref>PMID:10837477</ref> <ref>PMID:10995454</ref> <ref>PMID:11086004</ref> <ref>PMID:11486014</ref> <ref>PMID:14723849</ref> <ref>PMID:15743910</ref> <ref>PMID:17295840</ref> <ref>PMID:17426440</ref> <ref>PMID:17699586</ref> <ref>PMID:18077553</ref> <ref>PMID:18287526</ref> <ref>PMID:19805182</ref> <ref>PMID:19995911</ref> <ref>PMID:20439775</ref> <ref>PMID:20647741</ref> <ref>PMID:20855505</ref> <ref>PMID:21468027</ref> <ref>PMID:21712380</ref> <ref>PMID:22447937</ref> <ref>PMID:22778255</ref> <ref>PMID:22782902</ref> <ref>PMID:22885598</ref> <ref>PMID:8224160</ref>	+	[https://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6kbm" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6kbm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Autophagy-related protein 3D structures\|Autophagy-related protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lee, C~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Park, J~~]]	+	[[Category: Lee C]]
-	[[Category: ~~Armadillo repeat]]~~	+	[[Category: Park J]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Protein binding-protein transport complex~~]]	+

OCA at 07:12, 27 May 2020

OCA — Wed, 27 May 2020 07:12:31 GMT

←Older revision		Revision as of 07:12, 27 May 2020
Line 3:		Line 3:
	<StructureSection load='6kbm' size='340' side='right'caption='[[6kbm]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6kbm' size='340' side='right'caption='[[6kbm]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6kbm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KBM OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KBM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kbm]] is a 2 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=6KBM OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KBM FirstGlance]. <br>
-	</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=6kbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbm OCA], [http://pdbe.org/6kbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kbm RCSB], [http://www.ebi.ac.uk/pdbsum/6kbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbm ProSAT]</span></td></tr>	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6kbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbm OCA], [http://pdbe.org/6kbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kbm RCSB], [http://www.ebi.ac.uk/pdbsum/6kbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Lee, C]]		[[Category: Lee, C]]

OCA at 06:47, 27 November 2019

OCA — Wed, 27 Nov 2019 06:47:52 GMT

←Older revision		Revision as of 06:47, 27 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6kbm is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Vac8 bound to Atg13==
		+	<StructureSection load='6kbm' size='340' side='right'caption='[[6kbm]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6kbm]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KBM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KBM FirstGlance]. <br>
		+	</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=6kbm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kbm OCA], [http://pdbe.org/6kbm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kbm RCSB], [http://www.ebi.ac.uk/pdbsum/6kbm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kbm ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST]] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref> [[http://www.uniprot.org/uniprot/ATG13_YEAST ATG13_YEAST]] Activates the ATG1 kinase in a nutritional condition dependent manner through the TOR pathway, leading to autophagy. Required for autophosphorylation of ATG1 at 'Thr-226' and its dimerization. May also be involved in the regulation of autophagy through SNF1. Involved in ATG9 and ATG23 cycling through the pre-autophagosomal structure. Also involved in cytoplasm to vacuole transport (Cvt) and more specifically in Cvt vesicle formation. Seems to play a role in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage during stationary phase.<ref>PMID:10837477</ref> <ref>PMID:10995454</ref> <ref>PMID:11086004</ref> <ref>PMID:11486014</ref> <ref>PMID:14723849</ref> <ref>PMID:15743910</ref> <ref>PMID:17295840</ref> <ref>PMID:17426440</ref> <ref>PMID:17699586</ref> <ref>PMID:18077553</ref> <ref>PMID:18287526</ref> <ref>PMID:19805182</ref> <ref>PMID:19995911</ref> <ref>PMID:20439775</ref> <ref>PMID:20647741</ref> <ref>PMID:20855505</ref> <ref>PMID:21468027</ref> <ref>PMID:21712380</ref> <ref>PMID:22447937</ref> <ref>PMID:22778255</ref> <ref>PMID:22782902</ref> <ref>PMID:22885598</ref> <ref>PMID:8224160</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae. Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-A extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Delta19-33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways. Abbreviations : Ape1: aminopeptidase I; ARM: armadillo repeat; Atg: autophagy-related; AUC: analytical ultracentrifugation; Cvt: cytoplasm-to-vacuole targeting; DIC: differential interference contrast; GFP: green fluorescent protein; GST: glutathione-S-transferase; ITC: isothermal titration calorimetry; NVJ: nucleus-vacuole junction; PDB: protein data bank; PMN: piecemeal microautophagy of the nucleus; prApe1: precursor Ape1; RMSD: root-mean-square deviation; SAXS: small-angle X-ray scattering; SD-N: nitrogen starvation medium; SEC: size-exclusion chromatography; tAtg13: Atg13 construct comprising residues 567-695; tNvj1: Nvj1 construct comprising residues 229-321; tVac8: Vac8 construct comprising residues 10-515; Vac8: vacuole related 8.

-	~~Authors: Park~~, J., Lee, C.	+	Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.,Park J, Kim HI, Jeong H, Lee M, Jang SH, Yoon SY, Kim H, Park ZY, Jun Y, Lee C Autophagy. 2019 Sep 12:1-16. doi: 10.1080/15548627.2019.1659615. PMID:31512555<ref>PMID:31512555</ref>

-	~~Description: Crystal structure~~ of ~~Vac8 bound to Atg13~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6kbm" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lee, C]]		[[Category: Lee, C]]
	[[Category: Park, J]]		[[Category: Park, J]]
		+	[[Category: Armadillo repeat]]
		+	[[Category: Complex]]
		+	[[Category: Protein binding-protein transport complex]]

OCA at 06:31, 2 October 2019

OCA — Wed, 02 Oct 2019 06:31:30 GMT

←Older revision		Revision as of 06:31, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kbm is ON HOLD	+	The entry 6kbm is ON HOLD until Paper Publication

	Authors: Park, J., Lee, C.		Authors: Park, J., Lee, C.

OCA: Protected "6kbm" [edit=sysop:move=sysop]

OCA — Wed, 03 Jul 2019 04:06:57 GMT

Protected "6kbm" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:06, 3 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kbm is ON HOLD Authors: Park, J., Lee, C. Description: Crystal structure of Vac8 bound to Atg13 Category: Unreleased Structures [[Category: Le...

OCA — Wed, 03 Jul 2019 04:06:55 GMT

New page: '''Unreleased structure''' The entry 6kbm is ON HOLD Authors: Park, J., Lee, C. Description: Crystal structure of Vac8 bound to Atg13 Category: Unreleased Structures [[Category: Le...

New page

'''Unreleased structure'''

The entry 6kbm is ON HOLD

Authors: Park, J., Lee, C.

Description: Crystal structure of Vac8 bound to Atg13
[[Category: Unreleased Structures]]
[[Category: Lee, C]]
[[Category: Park, J]]