6hol - Revision history

OCA at 11:34, 24 January 2024

2024-01-24T11:34:55Z

←Older revision		Revision as of 11:34, 24 January 2024
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	<StructureSection load='6hol' size='340' side='right'caption='[[6hol]], [[Resolution\|resolution]] 1.40Å' scene=''>		<StructureSection load='6hol' size='340' side='right'caption='[[6hol]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hol]] 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=6HOL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hol]] 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=6HOL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HOL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.4Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GABARAPL1, GEC1 ([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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hol OCA], [~~http~~://pdbe.org/6hol PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hol RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hol PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hol 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=6hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hol OCA], [https://pdbe.org/6hol PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hol RCSB], [https://www.ebi.ac.uk/pdbsum/6hol PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hol ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GBRL1_HUMAN GBRL1_HUMAN]] Increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles.<ref>PMID:16431922</ref> <ref>PMID:20404487</ref> [[http://www.uniprot.org/uniprot/BAKOR_HUMAN BAKOR_HUMAN]] Required for both basal and inducible autophagy. Determines the localization of the autophagy-specific PI3-kinase complex PI3KC3-C1 (PubMed:18843052, PubMed:19050071). Plays a role in autophagosome formation and MAP1LC3/LC3 conjugation to phosphatidylethanolamine (PubMed:19270696, PubMed:20713597). Promotes BECN1 translocation from the trans-Golgi network to autophagosomes (PubMed:20713597). Enhances PIK3C3 activity in a BECN1-dependent manner. Essential for the autophagy-dependent phosphorylation of BECN1 (PubMed:23878393). Stimulates the phosphorylation of BECN1, but suppresses the phosphorylation PIK3C3 by AMPK (PubMed:23878393). Binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion (PubMed:25686604). Modulates the hepatic lipid metabolism (By similarity).[UniProtKB:Q8CDJ3]<ref>PMID:18843052</ref> <ref>PMID:19050071</ref> <ref>PMID:19270696</ref> <ref>PMID:20713597</ref> <ref>PMID:23878393</ref> <ref>PMID:25686604</ref>	+	[https://www.uniprot.org/uniprot/GBRL1_HUMAN GBRL1_HUMAN] Increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles.<ref>PMID:16431922</ref> <ref>PMID:20404487</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bhujbal, Z]]	+	[[Category: Bhujbal Z]]
-	[[Category: Birgisdottir~~, A B~~]]	+	[[Category: Birgisdottir AB]]
-	[[Category: Evjen, G]]	+	[[Category: Evjen G]]
-	[[Category: Johansen, T]]	+	[[Category: Johansen T]]
-	[[Category: Lamark, T]]	+	[[Category: Lamark T]]
-	[[Category: Lee, R]]	+	[[Category: Lee R]]
-	[[Category: Mouilleron, S]]	+	[[Category: Mouilleron S]]
-	[[Category: Reilly, N O]]	+	[[Category: O'Reilly N]]
-	[[Category: Sjottem, E]]	+	[[Category: Sjottem E]]
-	[[Category: Tooze, S]]	+	[[Category: Tooze S]]
-	[[Category: Wirth, M]]	+	[[Category: Wirth M]]
-	[[Category: Zhang, W]]	+	[[Category: Zhang W]]
-	~~[[Category: Atg8]]~~	+
-	~~[[Category: Autophagy]]~~	+
-	~~[[Category: Lir]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 06:22, 10 July 2019

2019-07-10T06:22:55Z

←Older revision		Revision as of 06:22, 10 July 2019
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	</div>		</div>
	<div class="pdbe-citations 6hol" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6hol" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[GABA receptor-associated protein 3D structures\|GABA receptor-associated protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:42, 13 March 2019

2019-03-13T12:42:16Z

←Older revision		Revision as of 12:42, 13 March 2019
Line 1:		Line 1:

	==Structure of ATG14 LIR motif bound to GABARAPL1==		==Structure of ATG14 LIR motif bound to GABARAPL1==
-	<StructureSection load='6hol' size='340' side='right' caption='[[6hol]], [[Resolution\|resolution]] 1.40Å' scene=''>	+	<StructureSection load='6hol' size='340' side='right'caption='[[6hol]], [[Resolution\|resolution]] 1.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hol]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HOL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hol]] 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=6HOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HOL FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABARAPL1, GEC1 ([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=6hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hol OCA], [http://pdbe.org/6hol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hol RCSB], [http://www.ebi.ac.uk/pdbsum/6hol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hol 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=6hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hol OCA], [http://pdbe.org/6hol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hol RCSB], [http://www.ebi.ac.uk/pdbsum/6hol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hol ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bhujbal, Z]]		[[Category: Bhujbal, Z]]
	[[Category: Birgisdottir, A B]]		[[Category: Birgisdottir, A B]]

OCA at 15:22, 27 February 2019

2019-02-27T15:22:53Z

←Older revision		Revision as of 15:22, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6hol is ~~ON HOLD~~	+	==Structure of ATG14 LIR motif bound to GABARAPL1==
		+	<StructureSection load='6hol' size='340' side='right' caption='[[6hol]], [[Resolution\|resolution]] 1.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hol]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HOL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HOL FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6hol FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hol OCA], [http://pdbe.org/6hol PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hol RCSB], [http://www.ebi.ac.uk/pdbsum/6hol PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hol ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GBRL1_HUMAN GBRL1_HUMAN]] Increases cell-surface expression of kappa-type opioid receptor through facilitating anterograde intracellular trafficking of the receptor. Involved in formation of autophagosomal vacuoles.<ref>PMID:16431922</ref> <ref>PMID:20404487</ref> [[http://www.uniprot.org/uniprot/BAKOR_HUMAN BAKOR_HUMAN]] Required for both basal and inducible autophagy. Determines the localization of the autophagy-specific PI3-kinase complex PI3KC3-C1 (PubMed:18843052, PubMed:19050071). Plays a role in autophagosome formation and MAP1LC3/LC3 conjugation to phosphatidylethanolamine (PubMed:19270696, PubMed:20713597). Promotes BECN1 translocation from the trans-Golgi network to autophagosomes (PubMed:20713597). Enhances PIK3C3 activity in a BECN1-dependent manner. Essential for the autophagy-dependent phosphorylation of BECN1 (PubMed:23878393). Stimulates the phosphorylation of BECN1, but suppresses the phosphorylation PIK3C3 by AMPK (PubMed:23878393). Binds to STX17-SNAP29 binary t-SNARE complex on autophagosomes and primes it for VAMP8 interaction to promote autophagosome-endolysosome fusion (PubMed:25686604). Modulates the hepatic lipid metabolism (By similarity).[UniProtKB:Q8CDJ3]<ref>PMID:18843052</ref> <ref>PMID:19050071</ref> <ref>PMID:19270696</ref> <ref>PMID:20713597</ref> <ref>PMID:23878393</ref> <ref>PMID:25686604</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 and ATG14 and phosphorylates phosphatidylinositol to generate phosphatidylinositol 3-phosphate (PtdIns3P). Here, we show that PIK3C3, BECN1 and ATG14 contain functional LIR motifs and interact with the Atg8-family proteins with a preference for GABARAP and GABARAPL1. High resolution crystal structures of the functional LIR motifs of these core components of PtdIns3K-C1were obtained. Variation in hydrophobic pocket 2 (HP2) may explain the specificity for the GABARAP family. Mutation of the LIR motif in ATG14 did not prevent formation of the PtdIns3K-C1 complex, but blocked colocalization with MAP1LC3B/LC3B and impaired mitophagy. The ULK-mediated phosphorylation of S29 in ATG14 was strongly dependent on a functional LIR motif in ATG14. GABARAP-preferring LIR motifs in PIK3C3, BECN1 and ATG14 may, via coincidence detection, contribute to scaffolding of PtdIns3K-C1 on membranes for efficient autophagosome formation.

-	~~Authors: Mouilleron, S~~., Birgisdottir, ~~A.B., Bhujbal~~, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze~~, S.~~, Lamark, T., Johansen, T.	+	Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.,Birgisdottir AB, Mouilleron S, Bhujabal Z, Wirth M, Sjottem E, Evjen G, Zhang W, Lee R, O'Reilly N, Tooze SA, Lamark T, Johansen T Autophagy. 2019 Feb 15. doi: 10.1080/15548627.2019.1581009. PMID:30767700<ref>PMID:30767700</ref>

-	~~Description: Structure~~ of ~~ATG14 LIR motif bound to GABARAPL1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Lamark, T]]~~	+	<div class="pdbe-citations 6hol" style="background-color:#fffaf0;"></div>
-	~~[[Category: Lee, R]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bhujbal, Z]]		[[Category: Bhujbal, Z]]
-	[[Category: ~~O'Reilly~~, ~~N]]~~	+	[[Category: Birgisdottir, A B]]
-	~~[[Category: Tooze, S~~]]	+
	[[Category: Evjen, G]]		[[Category: Evjen, G]]
	[[Category: Johansen, T]]		[[Category: Johansen, T]]
-	[[Category: ~~Sjottem~~, E]]	+	[[Category: Lamark, T]]
		+	[[Category: Lee, R]]
	[[Category: Mouilleron, S]]		[[Category: Mouilleron, S]]
-	[[Category: ~~Zhang~~, W]]	+	[[Category: Reilly, N O]]
		+	[[Category: Sjottem, E]]
		+	[[Category: Tooze, S]]
	[[Category: Wirth, M]]		[[Category: Wirth, M]]
-	[[Category: ~~Birgisdottir~~, ~~A.B~~]]	+	[[Category: Zhang, W]]
		+	[[Category: Atg8]]
		+	[[Category: Autophagy]]
		+	[[Category: Lir]]
		+	[[Category: Signaling protein]]

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

2018-09-26T06:15:43Z

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

←Older revision

Revision as of 06:15, 26 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hol is ON HOLD Authors: Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze...

2018-09-26T06:15:42Z

New page: '''Unreleased structure''' The entry 6hol is ON HOLD Authors: Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze...

New page

'''Unreleased structure'''

The entry 6hol is ON HOLD

Authors: Mouilleron, S., Birgisdottir, A.B., Bhujbal, Z., Wirth, M., Sjottem, E., Evjen, G., Zhang, W., Lee, R., O'Reilly, N., Tooze, S., Lamark, T., Johansen, T.

Description: Structure of ATG14 LIR motif bound to GABARAPL1
[[Category: Unreleased Structures]]
[[Category: Lamark, T]]
[[Category: Lee, R]]
[[Category: Bhujbal, Z]]
[[Category: O'Reilly, N]]
[[Category: Tooze, S]]
[[Category: Evjen, G]]
[[Category: Johansen, T]]
[[Category: Sjottem, E]]
[[Category: Mouilleron, S]]
[[Category: Zhang, W]]
[[Category: Wirth, M]]
[[Category: Birgisdottir, A.B]]