5kc1 - Revision history

OCA at 10:44, 27 September 2023

OCA — Wed, 27 Sep 2023 10:44:40 GMT

←Older revision		Revision as of 10:44, 27 September 2023
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	<StructureSection load='5kc1' size='340' side='right'caption='[[5kc1]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='5kc1' size='340' side='right'caption='[[5kc1]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5KC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kc1]] is a 12 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=5KC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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]] 2.2Å</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=5kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc1 OCA], [~~http~~://pdbe.org/5kc1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5kc1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5kc1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc1 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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'>[https://proteopedia.org/fgij/fg.htm?mol=5kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc1 OCA], [https://pdbe.org/5kc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kc1 RCSB], [https://www.ebi.ac.uk/pdbsum/5kc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATG38_YEAST ATG38_YEAST]] Autophagy-related protein required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. ATG38 is required for the integrity of the active PI3-kinase complex I by maintaining an association between VPS15-VPS34 and ATG1P-VPS30 subcomplexes.<ref>PMID:24165940</ref>	+	[https://www.uniprot.org/uniprot/ATG38_YEAST ATG38_YEAST] Autophagy-related protein required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. ATG38 is required for the integrity of the active PI3-kinase complex I by maintaining an association between VPS15-VPS34 and ATG1P-VPS30 subcomplexes.<ref>PMID:24165940</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Garcia-Ortegon, M]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Johnson~~, C M~~]]	+	[[Category: Garcia-Ortegon M]]
-	[[Category: Masson~~, G R~~]]	+	[[Category: Johnson CM]]
-	[[Category: Ohashi, Y]]	+	[[Category: Masson GR]]
-	[[Category: Perisic, O]]	+	[[Category: Ohashi Y]]
-	[[Category: Soler, N]]	+	[[Category: Perisic O]]
-	[[Category: Williams~~, R J~~]]	+	[[Category: Soler N]]
-	[[Category: Zhang, L]]	+	[[Category: Williams RJ]]
-	~~[[Category: Atg38]]~~	+	[[Category: Zhang L]]
-	~~[[Category: Autophagy]]~~	+
-	~~[[Category: Coiled-coil]]~~	+
-	~~[[Category: Dimerization]]~~	+
-	~~[[Category: Endocytosis]]~~	+
-	~~[[Category: Nrbf2~~]]	+

OCA at 09:32, 1 July 2020

OCA — Wed, 01 Jul 2020 09:32:46 GMT

←Older revision		Revision as of 09:32, 1 July 2020
Line 1:		Line 1:

	==Structure of the C-terminal dimerization domain of Atg38==		==Structure of the C-terminal dimerization domain of Atg38==
-	<StructureSection load='5kc1' size='340' side='right' caption='[[5kc1]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='5kc1' size='340' side='right'caption='[[5kc1]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5kc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC1 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5KC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5kc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC1 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5KC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=5kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc1 OCA], [http://pdbe.org/5kc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc1 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc1 ProSAT]</span></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=5kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc1 OCA], [http://pdbe.org/5kc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc1 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Garcia-Ortegon, M]]		[[Category: Garcia-Ortegon, M]]
	[[Category: Johnson, C M]]		[[Category: Johnson, C M]]

OCA at 21:32, 5 October 2016

OCA — Wed, 05 Oct 2016 21:32:56 GMT

←Older revision		Revision as of 21:32, 5 October 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5kc1 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of the C-terminal dimerization domain of Atg38==
		+	<StructureSection load='5kc1' size='340' side='right' caption='[[5kc1]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5kc1]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KC1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NH4:AMMONIUM+ION'>NH4</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</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=5kc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kc1 OCA], [http://pdbe.org/5kc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kc1 RCSB], [http://www.ebi.ac.uk/pdbsum/5kc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kc1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATG38_YEAST ATG38_YEAST]] Autophagy-related protein required for cytoplasm to vacuole transport (Cvt) and autophagy as a part of the autophagy-specific VPS34 PI3-kinase complex I. This complex is essential to recruit the ATG8-phosphatidylinositol conjugate and the ATG12-ATG5 conjugate to the pre-autophagosomal structure. ATG38 is required for the integrity of the active PI3-kinase complex I by maintaining an association between VPS15-VPS34 and ATG1P-VPS30 subcomplexes.<ref>PMID:24165940</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 A resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of alpha-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.

-	~~Authors~~:	+	Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.,Ohashi Y, Soler N, Garcia Ortegon M, Zhang L, Kirsten ML, Perisic O, Masson GR, Burke JE, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL Autophagy. 2016 Sep 14:0. PMID:27630019<ref>PMID:27630019</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5kc1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Garcia-Ortegon, M]]
		+	[[Category: Johnson, C M]]
		+	[[Category: Masson, G R]]
		+	[[Category: Ohashi, Y]]
		+	[[Category: Perisic, O]]
		+	[[Category: Soler, N]]
		+	[[Category: Williams, R J]]
		+	[[Category: Zhang, L]]
		+	[[Category: Atg38]]
		+	[[Category: Autophagy]]
		+	[[Category: Coiled-coil]]
		+	[[Category: Dimerization]]
		+	[[Category: Endocytosis]]
		+	[[Category: Nrbf2]]

OCA: Protected "5kc1" [edit=sysop:move=sysop]

OCA — Mon, 20 Jun 2016 13:42:19 GMT

Protected "5kc1" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:42, 20 June 2016

OCA: New page: '''Unreleased structure''' The entry 5kc1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Mon, 20 Jun 2016 13:42:18 GMT

New page: '''Unreleased structure''' The entry 5kc1 is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5kc1 is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]