5jgf - Revision history

OCA at 11:03, 6 September 2023

OCA — Wed, 06 Sep 2023 11:03:11 GMT

←Older revision		Revision as of 11:03, 6 September 2023
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	<StructureSection load='5jgf' size='340' side='right'caption='[[5jgf]], [[Resolution\|resolution]] 1.83Å' scene=''>		<StructureSection load='5jgf' size='340' side='right'caption='[[5jgf]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jgf]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5JGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jgf]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5JGF FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.83Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">APE1, API, LAP4, YSC1, YKL103C, YKL455 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=559292 Baker's yeast])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[http://en.wikipedia.org/wiki/Aminopeptidase_I Aminopeptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.22 3.4.11.22]~~ </~~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=5jgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgf OCA], [https://pdbe.org/5jgf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5jgf RCSB], [https://www.ebi.ac.uk/pdbsum/5jgf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgf 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=5jgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgf OCA], [~~http~~://pdbe.org/5jgf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5jgf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5jgf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgf ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AMPL_YEAST AMPL_YEAST]] Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:15138258</ref> <ref>PMID:22123825</ref> <ref>PMID:363165</ref> <ref>PMID:8901576</ref> <ref>PMID:9214379</ref> <ref>PMID:9412464</ref>	+	[https://www.uniprot.org/uniprot/AMPL_YEAST AMPL_YEAST] Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:15138258</ref> <ref>PMID:22123825</ref> <ref>PMID:363165</ref> <ref>PMID:8901576</ref> <ref>PMID:9214379</ref> <ref>PMID:9412464</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: Aminopeptidase I]]
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Adachi, W~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Inagaki, F~~]]	+	[[Category: Adachi W]]
-	[[Category: ~~Noda, N N~~]]	+	[[Category: Inagaki F]]
-	[[Category: ~~Hydrolase]]~~	+	[[Category: Noda NN]]
-	~~[[Category: Tetrahedral dodecamer~~]]	+

OCA at 07:18, 19 February 2020

OCA — Wed, 19 Feb 2020 07:18:26 GMT

←Older revision		Revision as of 07:18, 19 February 2020
Line 1:		Line 1:

	==Crystal structure of mApe1==		==Crystal structure of mApe1==
-	<StructureSection load='5jgf' size='340' side='right' caption='[[5jgf]], [[Resolution\|resolution]] 1.83Å' scene=''>	+	<StructureSection load='5jgf' size='340' side='right'caption='[[5jgf]], [[Resolution\|resolution]] 1.83Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5jgf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5jgf]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGF FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">APE1, API, LAP4, YSC1, YKL103C, YKL455 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminopeptidase_I Aminopeptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.22 3.4.11.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminopeptidase_I Aminopeptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.22 3.4.11.22] </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=5jgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgf OCA], [http://pdbe.org/5jgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jgf RCSB], [http://www.ebi.ac.uk/pdbsum/5jgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgf 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=5jgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgf OCA], [http://pdbe.org/5jgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jgf RCSB], [http://www.ebi.ac.uk/pdbsum/5jgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgf ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5jgf" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5jgf" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Aminopeptidase I]]		[[Category: Aminopeptidase I]]
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Adachi, W]]		[[Category: Adachi, W]]
	[[Category: Inagaki, F]]		[[Category: Inagaki, F]]

OCA at 02:59, 13 July 2016

OCA — Wed, 13 Jul 2016 02:59:26 GMT

←Older revision		Revision as of 02:59, 13 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5jgf is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of mApe1==
		+	<StructureSection load='5jgf' size='340' side='right' caption='[[5jgf]], [[Resolution\|resolution]] 1.83Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5jgf]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5JGF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5JGF FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aminopeptidase_I Aminopeptidase I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.22 3.4.11.22] </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=5jgf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5jgf OCA], [http://pdbe.org/5jgf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5jgf RCSB], [http://www.ebi.ac.uk/pdbsum/5jgf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5jgf ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPL_YEAST AMPL_YEAST]] Resident vacuolar enzyme that catalyzes the removal of amino acids from the N-terminus of peptides and proteins. Also acts as the major cargo protein of the cytoplasm-to-vacuole targeting (Cvt) pathway. The precursor form of aminopeptidase 1 (prApe1) assembles into dodecamers and the propeptide mediates the aggregation of dodecamers into higher multimers. The multimers are then recognized via the propeptide by their receptor ATG19, and ATG19 further interacts with ATG11, which tethers the APE1-ATG19 complex to the pre-autophagosomal structure (PAS). The cargo-receptor complex (also Cvt complex) is selectively enwrapped by a double-membrane structure termed the Cvt vesicle under vegetative growth conditions and by a similar but larger double-membrane structure termed the autophagosome under nitrogen starvation conditions. The Cvt vesicle or the autophagosome fuses with the vacuolar membrane and release its content in the vacuolar lumen. In the vacuole, prApe1 is processed into mature aminopeptidase 1 (mApe1).<ref>PMID:11382752</ref> <ref>PMID:11430817</ref> <ref>PMID:15138258</ref> <ref>PMID:22123825</ref> <ref>PMID:363165</ref> <ref>PMID:8901576</ref> <ref>PMID:9214379</ref> <ref>PMID:9412464</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Selective autophagy mediates the degradation of various cargoes, including protein aggregates and organelles, thereby contributing to cellular homeostasis. Cargo receptors ensure selectivity by tethering specific cargo to lipidated Atg8 at the isolation membrane. However, little is known about the structural requirements underlying receptor-mediated cargo recognition. Here, we report structural, biochemical, and cell biological analysis of the major selective cargo protein in budding yeast, aminopeptidase I (Ape1), and its complex with the receptor Atg19. The Ape1 propeptide has a trimeric coiled-coil structure, which tethers dodecameric Ape1 bodies together to form large aggregates. Atg19 disassembles the propeptide trimer and forms a 2:1 heterotrimer, which not only blankets the Ape1 aggregates but also regulates their size. These receptor activities may promote elongation of the isolation membrane along the aggregate surface, enabling sequestration of the cargo with high specificity.

-	~~Authors: Noda, N.N~~., ~~Adachi~~, W., ~~Inagaki~~, F.	+	Structural Basis for Receptor-Mediated Selective Autophagy of Aminopeptidase I Aggregates.,Yamasaki A, Watanabe Y, Adachi W, Suzuki K, Matoba K, Kirisako H, Kumeta H, Nakatogawa H, Ohsumi Y, Inagaki F, Noda NN Cell Rep. 2016 Jun 28;16(1):19-27. doi: 10.1016/j.celrep.2016.05.066. Epub 2016, Jun 16. PMID:27320913<ref>PMID:27320913</ref>

-	~~Description: Crystal structure~~ of ~~mApe1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5jgf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Aminopeptidase I]]
	[[Category: Adachi, W]]		[[Category: Adachi, W]]
	[[Category: Inagaki, F]]		[[Category: Inagaki, F]]
-	[[Category: Noda, N.N]]	+	[[Category: Noda, N N]]
		+	[[Category: Hydrolase]]
		+	[[Category: Tetrahedral dodecamer]]

OCA at 13:23, 1 June 2016

OCA — Wed, 01 Jun 2016 13:23:57 GMT

←Older revision		Revision as of 13:23, 1 June 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5jgf is ON HOLD until ~~sometime in the future~~	+	The entry 5jgf is ON HOLD until Paper Publication

	Authors: Noda, N.N., Adachi, W., Inagaki, F.		Authors: Noda, N.N., Adachi, W., Inagaki, F.

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

OCA — Wed, 11 May 2016 02:01:05 GMT

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

←Older revision

Revision as of 02:01, 11 May 2016

OCA: New page: '''Unreleased structure''' The entry 5jgf is ON HOLD until sometime in the future Authors: Noda, N.N., Adachi, W., Inagaki, F. Description: Crystal structure of mApe1 [[Category: Unrel...

OCA — Wed, 11 May 2016 02:01:04 GMT

New page: '''Unreleased structure''' The entry 5jgf is ON HOLD until sometime in the future Authors: Noda, N.N., Adachi, W., Inagaki, F. Description: Crystal structure of mApe1 [[Category: Unrel...

New page

'''Unreleased structure'''

The entry 5jgf is ON HOLD until sometime in the future

Authors: Noda, N.N., Adachi, W., Inagaki, F.

Description: Crystal structure of mApe1
[[Category: Unreleased Structures]]
[[Category: Adachi, W]]
[[Category: Inagaki, F]]
[[Category: Noda, N.N]]