5xv3 - Revision history

OCA at 08:14, 22 November 2023

OCA — Wed, 22 Nov 2023 08:14:36 GMT

←Older revision		Revision as of 08:14, 22 November 2023
Line 1:		Line 1:

	==Crystal structure of ATG101-ATG13HORMA==		==Crystal structure of ATG101-ATG13HORMA==
-	<StructureSection load='5xv3' size='340' side='right' caption='[[5xv3]], [[Resolution\|resolution]] 2.57Å' scene=''>	+	<StructureSection load='5xv3' size='340' side='right'caption='[[5xv3]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xv3]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xv3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XV3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.57Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ATG13, KIAA0652 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]~~)~~, ATG101, C12orf44, PP894 ([http:~~/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5xv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv3 OCA], [~~http~~://pdbe.org/5xv3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xv3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xv3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv3 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=5xv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv3 OCA], [https://pdbe.org/5xv3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xv3 RCSB], [https://www.ebi.ac.uk/pdbsum/5xv3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATG13_HUMAN ATG13_HUMAN]] Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.<ref>PMID:19287211</ref> <ref>PMID:19211835</ref> <ref>PMID:19225151</ref> <ref>PMID:21855797</ref> <ref>PMID:18936157</ref> <ref>PMID:21795849</ref> [[http://www.uniprot.org/uniprot/ATGA1_HUMAN ATGA1_HUMAN]] Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation.<ref>PMID:19287211</ref> <ref>PMID:19597335</ref>	+	[https://www.uniprot.org/uniprot/ATG13_HUMAN ATG13_HUMAN] Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.<ref>PMID:19287211</ref> <ref>PMID:19211835</ref> <ref>PMID:19225151</ref> <ref>PMID:21855797</ref> <ref>PMID:18936157</ref> <ref>PMID:21795849</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Kim, B W~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Song, H K~~]]	+	[[Category: Kim B-W]]
-	[[Category: ~~Atg101]]~~	+	[[Category: Song HK]]
-	~~[[Category: Atg13]]~~	+
-	~~[[Category: Autophagy]]~~	+
-	~~[[Category: Horma]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 12:25, 16 January 2019

OCA — Wed, 16 Jan 2019 12:25:38 GMT

←Older revision		Revision as of 12:25, 16 January 2019
Line 3:		Line 3:
	<StructureSection load='5xv3' size='340' side='right' caption='[[5xv3]], [[Resolution\|resolution]] 2.57Å' scene=''>		<StructureSection load='5xv3' size='340' side='right' caption='[[5xv3]], [[Resolution\|resolution]] 2.57Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xv3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xv3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ATG13, KIAA0652 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), ATG101, C12orf44, PP894 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=5xv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv3 OCA], [http://pdbe.org/5xv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv3 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=5xv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv3 OCA], [http://pdbe.org/5xv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ATG13_HUMAN ATG13_HUMAN]] Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.<ref>PMID:19287211</ref> <ref>PMID:19211835</ref> <ref>PMID:19225151</ref> <ref>PMID:21855797</ref> <ref>PMID:18936157</ref> <ref>PMID:21795849</ref> [[http://www.uniprot.org/uniprot/ATGA1_HUMAN ATGA1_HUMAN]] Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation.<ref>PMID:19287211</ref> <ref>PMID:19597335</ref>		[[http://www.uniprot.org/uniprot/ATG13_HUMAN ATG13_HUMAN]] Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.<ref>PMID:19287211</ref> <ref>PMID:19211835</ref> <ref>PMID:19225151</ref> <ref>PMID:21855797</ref> <ref>PMID:18936157</ref> <ref>PMID:21795849</ref> [[http://www.uniprot.org/uniprot/ATGA1_HUMAN ATGA1_HUMAN]] Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation.<ref>PMID:19287211</ref> <ref>PMID:19597335</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The initiation of macroautophagy/autophagy is tightly regulated by the upstream ULK1 kinase complex, which affects many downstream factors including the PtdIns3K complex. The phosphorylation of the right position at the right time on downstream molecules is governed by proper complex formation. One component of the ULK1 complex, ATG101, known as an accessory protein, is a stabilizer of ATG13 in cells. The WF finger region of ATG101 plays an important role in the recruitment of WIPI1 (WD repeat domain, phosphoinositide interacting protein 1) and ZFYVE1 (zinc finger FYVE-type containing 1). Here, we report that the C-terminal region identified in the structure of the human ATG101-ATG13(HORMA) complex is responsible for the binding of the PtdIns3K complex. This region adopts a beta-strand conformation in free ATG101, but either an alpha-helix or random coil in our ATG101-ATG13(HORMA) complex, which protrudes from the core and interacts with other molecules. The C-terminal deletion of ATG101 shows a significant defect in the interaction with PtdIns3K components and subsequently impairs autophagosome formation. This result clearly presents an additional role of ATG101 for bridging the ULK1 and PtdIns3K complexes in the mammalian autophagy process. Abbreviations: ATG: autophagy related; BECN1: beclin 1; GFP: green fluorescent protein; HORMA: Hop1p/Rev7p/MAD2; HsATG13(HORMA): HORMA domain of ATG13 from Homo sapiens; KO: knockout; MAD2: mitotic arrest deficient 2 like 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; PIK3C3/VPS34: phosphatidylinositol 3-kinase catalytic subunit type 3; PIK3R4/VPS15: phosphoinositide-3-kinase regulatory subunit 4; PtdIns3K: phosphatidylinositol 3-kinase; RB1CC1/FIP200: RB1 inducible coiled-coil 1; SAXS: small-angle X-ray scattering; ScAtg13(HORMA): HORMA domain of Atg13 from Sccharomyces cerevisiae; SEC-SAXS: size-exclusion chromatography with small-angle X-ray scattering; SpAtg13(HORMA): HORMA domain of Atg13 from Schizosaccharomyces pombe; SQSTM1/p62: sequestosome 1; ULK1: unc51-like autophagy activating kinase 1; UVRAG: UV radiation resistance associated; WIPI1: WD repeat domain: phosphoinositide interacting 1; ZFYVE1/DFCP1: zinc finger FYVE-type containing 1.
		+
		+	The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation.,Kim BW, Jin Y, Kim J, Kim JH, Jung J, Kang S, Kim IY, Kim J, Cheong H, Song HK Autophagy. 2018;14(12):2104-2116. doi: 10.1080/15548627.2018.1504716. Epub 2018, Aug 16. PMID:30081750<ref>PMID:30081750</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xv3" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Kim, B W]]		[[Category: Kim, B W]]
	[[Category: Song, H K]]		[[Category: Song, H K]]

OCA at 07:07, 4 July 2018

OCA — Wed, 04 Jul 2018 07:07:18 GMT

←Older revision		Revision as of 07:07, 4 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xv3 is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of ATG101-ATG13HORMA==
-		+	<StructureSection load='5xv3' size='340' side='right' caption='[[5xv3]], [[Resolution\|resolution]] 2.57Å' scene=''>
-	~~Authors~~: ~~Kim~~, B.-W., ~~Song~~, H.K.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xv3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XV3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XV3 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure~~ of ~~ATG101~~-~~ATG13HORMA~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5xv3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xv3 OCA], [http://pdbe.org/5xv3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xv3 RCSB], [http://www.ebi.ac.uk/pdbsum/5xv3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xv3 ProSAT]</span></td></tr>
-	[[Category: Kim, B.-W]]	+	</table>
-	[[Category: Song, H.K]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATG13_HUMAN ATG13_HUMAN]] Autophagy factor required for autophagosome formation and mitophagy. Target of the TOR kinase signaling pathway that regulates autophagy through the control of the phosphorylation status of ATG13 and ULK1, and the regulation of the ATG13-ULK1-RB1CC1 complex. Through its regulation of ULK1 activity, plays a role in the regulation of the kinase activity of mTORC1 and cell proliferation.<ref>PMID:19287211</ref> <ref>PMID:19211835</ref> <ref>PMID:19225151</ref> <ref>PMID:21855797</ref> <ref>PMID:18936157</ref> <ref>PMID:21795849</ref> [[http://www.uniprot.org/uniprot/ATGA1_HUMAN ATGA1_HUMAN]] Autophagy factor required for autophagosome formation. Stabilizes ATG13, protecting it from proteasomal degradation.<ref>PMID:19287211</ref> <ref>PMID:19597335</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Kim, B W]]
		+	[[Category: Song, H K]]
		+	[[Category: Atg101]]
		+	[[Category: Atg13]]
		+	[[Category: Autophagy]]
		+	[[Category: Horma]]
		+	[[Category: Protein binding]]

OCA: Protected "5xv3" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 15:48:45 GMT

Protected "5xv3" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:48, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xv3 is ON HOLD until Paper Publication Authors: Kim, B.-W., Song, H.K. Description: Crystal structure of ATG101-ATG13HORMA [[Category: Unreleased ...

OCA — Wed, 27 Sep 2017 15:48:44 GMT

New page: '''Unreleased structure''' The entry 5xv3 is ON HOLD until Paper Publication Authors: Kim, B.-W., Song, H.K. Description: Crystal structure of ATG101-ATG13HORMA [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 5xv3 is ON HOLD until Paper Publication

Authors: Kim, B.-W., Song, H.K.

Description: Crystal structure of ATG101-ATG13HORMA
[[Category: Unreleased Structures]]
[[Category: Kim, B.-W]]
[[Category: Song, H.K]]