7d0i - Revision history

OCA at 10:52, 27 March 2024

OCA — Wed, 27 Mar 2024 10:52:38 GMT

←Older revision		Revision as of 10:52, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='7d0i' size='340' side='right'caption='[[7d0i]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='7d0i' size='340' side='right'caption='[[7d0i]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7d0i]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Fission_yeast Fission yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D0I OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7D0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d0i]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7D0I FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=LMN:LAURYL+MALTOSE+NEOPENTYL+GLYCOL'>LMN</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~atg9, apg9, SPBC15D4.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=284812 Fission yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LMN:LAURYL+MALTOSE+NEOPENTYL+GLYCOL'>LMN</scene></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=7d0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d0i OCA], [~~http~~://pdbe.org/7d0i PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7d0i RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7d0i PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7d0i 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=7d0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d0i OCA], [https://pdbe.org/7d0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7d0i RCSB], [https://www.ebi.ac.uk/pdbsum/7d0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7d0i ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/ATG9_SCHPO ATG9_SCHPO]] Involved in autophagy and cytoplasm to vacuole transport (Cvt) vesicle formation. Plays a key role in the organization of the preautophagosomal structure/phagophore assembly site (PAS), the nucleating site for formation of the sequestering vesicle. Required for mitophagy. Cycles between the PAS and the cytoplasmic vesicle pool and may participate in supplying membrane for the growing autophagosome. Also involved in endoplasmic reticulum-specific autophagic process and is essential for the survival of cells subjected to severe ER stress. Different machineries are required for anterograde trafficking to the PAS during either the Cvt pathway or bulk autophagy and for retrograde trafficking (By similarity). Has a role in meiosis and sporulation.[UniProtKB:Q12142]<ref>PMID:19778961</ref>	+	[https://www.uniprot.org/uniprot/ATG9_SCHPO ATG9_SCHPO] Involved in autophagy and cytoplasm to vacuole transport (Cvt) vesicle formation. Plays a key role in the organization of the preautophagosomal structure/phagophore assembly site (PAS), the nucleating site for formation of the sequestering vesicle. Required for mitophagy. Cycles between the PAS and the cytoplasmic vesicle pool and may participate in supplying membrane for the growing autophagosome. Also involved in endoplasmic reticulum-specific autophagic process and is essential for the survival of cells subjected to severe ER stress. Different machineries are required for anterograde trafficking to the PAS during either the Cvt pathway or bulk autophagy and for retrograde trafficking (By similarity). Has a role in meiosis and sporulation.[UniProtKB:Q12142]<ref>PMID:19778961</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion.	+

-	Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.,Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN Nat Struct Mol Biol. 2020 Oct 26. pii: 10.1038/s41594-020-00518-w. doi:, 10.1038/s41594-020-00518-w. PMID:33106658<ref>PMID:33106658</ref>	+	==See Also==
-		+	*[[Autophagy-related protein 3D structures\|Autophagy-related protein 3D structures]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe~~-~~citations 7d0i" style="background~~-~~color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kikkawa, M]]	+	[[Category: Schizosaccharomyces pombe 972h-]]
-	[[Category: Matoba, K]]	+	[[Category: Kikkawa M]]
-	[[Category: Noda~~, N N~~]]	+	[[Category: Matoba K]]
-	[[Category: Tsutsumi, A]]	+	[[Category: Noda NN]]
-	~~[[Category: Autophagy]]~~	+	[[Category: Tsutsumi A]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 08:18, 11 November 2020

OCA — Wed, 11 Nov 2020 08:18:16 GMT

←Older revision		Revision as of 08:18, 11 November 2020
Line 1:		Line 1:

	==Cryo-EM structure of Schizosaccharomyces pombe Atg9==		==Cryo-EM structure of Schizosaccharomyces pombe Atg9==
-	<StructureSection load='7d0i' size='340' side='right'caption='[[7d0i]]' scene=''>	+	<StructureSection load='7d0i' size='340' side='right'caption='[[7d0i]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D0I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D0I FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7d0i]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D0I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D0I 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=7d0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d0i OCA], [http://pdbe.org/7d0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d0i RCSB], [http://www.ebi.ac.uk/pdbsum/7d0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d0i ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LMN:LAURYL+MALTOSE+NEOPENTYL+GLYCOL'>LMN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">atg9, apg9, SPBC15D4.07c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</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=7d0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d0i OCA], [http://pdbe.org/7d0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d0i RCSB], [http://www.ebi.ac.uk/pdbsum/7d0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d0i ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ATG9_SCHPO ATG9_SCHPO]] Involved in autophagy and cytoplasm to vacuole transport (Cvt) vesicle formation. Plays a key role in the organization of the preautophagosomal structure/phagophore assembly site (PAS), the nucleating site for formation of the sequestering vesicle. Required for mitophagy. Cycles between the PAS and the cytoplasmic vesicle pool and may participate in supplying membrane for the growing autophagosome. Also involved in endoplasmic reticulum-specific autophagic process and is essential for the survival of cells subjected to severe ER stress. Different machineries are required for anterograde trafficking to the PAS during either the Cvt pathway or bulk autophagy and for retrograde trafficking (By similarity). Has a role in meiosis and sporulation.[UniProtKB:Q12142]<ref>PMID:19778961</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The molecular function of Atg9, the sole transmembrane protein in the autophagosome-forming machinery, remains unknown. Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER). Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro. Cryo-EM of fission yeast Atg9 reveals a homotrimer, with two connected pores forming a path between the two membrane leaflets: one pore, located at a protomer, opens laterally to the cytoplasmic leaflet; the other, at the trimer center, traverses the membrane vertically. Mutation of residues lining the pores impaired IM expansion and autophagy activity in yeast and abolished Atg9's ability to transport phospholipids between liposome leaflets. These results suggest that phospholipids delivered by Atg2 are translocated from the cytoplasmic to the luminal leaflet by Atg9, thereby driving autophagosomal membrane expansion.
		+
		+	Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.,Matoba K, Kotani T, Tsutsumi A, Tsuji T, Mori T, Noshiro D, Sugita Y, Nomura N, Iwata S, Ohsumi Y, Fujimoto T, Nakatogawa H, Kikkawa M, Noda NN Nat Struct Mol Biol. 2020 Oct 26. pii: 10.1038/s41594-020-00518-w. doi:, 10.1038/s41594-020-00518-w. PMID:33106658<ref>PMID:33106658</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7d0i" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Fission yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kikkawa M]]	+	[[Category: Kikkawa, M]]
-	[[Category: Matoba K]]	+	[[Category: Matoba, K]]
-	[[Category: Noda NN]]	+	[[Category: Noda, N N]]
-	[[Category: Tsutsumi A]]	+	[[Category: Tsutsumi, A]]
		+	[[Category: Autophagy]]
		+	[[Category: Membrane protein]]
		+	[[Category: Unknown function]]

OCA at 20:38, 28 October 2020

OCA — Wed, 28 Oct 2020 20:38:00 GMT

←Older revision		Revision as of 20:38, 28 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7d0i is ~~ON HOLD until Paper Publication~~	+	==Cryo-EM structure of Schizosaccharomyces pombe Atg9==
-		+	<StructureSection load='7d0i' size='340' side='right'caption='[[7d0i]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7D0I OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7D0I FirstGlance]. <br>
-	~~Description~~:	+	</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=7d0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7d0i OCA], [http://pdbe.org/7d0i PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7d0i RCSB], [http://www.ebi.ac.uk/pdbsum/7d0i PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7d0i ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Kikkawa M]]
		+	[[Category: Matoba K]]
		+	[[Category: Noda NN]]
		+	[[Category: Tsutsumi A]]

OCA at 04:09, 14 October 2020

OCA — Wed, 14 Oct 2020 04:09:09 GMT

←Older revision		Revision as of 04:09, 14 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7d0i is ON HOLD	+	The entry 7d0i is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7d0i" [edit=sysop:move=sysop]

OCA — Wed, 16 Sep 2020 06:57:06 GMT

Protected "7d0i" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:57, 16 September 2020

OCA: New page: '''Unreleased structure''' The entry 7d0i is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 16 Sep 2020 06:57:04 GMT

New page: '''Unreleased structure''' The entry 7d0i is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7d0i is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]