5xjg - Revision history

OCA at 10:18, 27 March 2024

OCA — Wed, 27 Mar 2024 10:18:50 GMT

←Older revision		Revision as of 10:18, 27 March 2024
Line 1:		Line 1:

	==Crystal structure of Vac8p bound to Nvj1p==		==Crystal structure of Vac8p bound to Nvj1p==
-	<StructureSection load='5xjg' size='340' side='right' caption='[[5xjg]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5xjg' size='340' side='right'caption='[[5xjg]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xjg]] 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=5XJG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XJG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xjg]] 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=5XJG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XJG FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</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]] 2.4Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VAC8, YEB3, YEL013W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), NVJ1, VAB36, YHR195W ([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=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</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=5xjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xjg OCA], [~~http~~://pdbe.org/5xjg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xjg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xjg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xjg 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=5xjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xjg OCA], [https://pdbe.org/5xjg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xjg RCSB], [https://www.ebi.ac.uk/pdbsum/5xjg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xjg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST]] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref> [[http://www.uniprot.org/uniprot/NVJ1_YEAST NVJ1_YEAST]] Involved in the formation of nucleus-vacuole (NV) junctions during piecemeal microautophagy of the nucleus (PMN). NV junctions are interorganelle interfaces mediated by NVJ1 in the nuclear envelope and VAC8 on the vacuole membrane. Together, NVJ1 and VAC8 form Velcro-like patches through which teardrop-like portions of the nucleus are pinched off into the vacuolar lumen and degraded by the PMN process. Acts also as an outer-nuclear membrane receptor for OSH1 and TSC13.<ref>PMID:10888680</ref> <ref>PMID:12529432</ref> <ref>PMID:15367582</ref> <ref>PMID:15958487</ref> <ref>PMID:16912077</ref>	+	[https://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Formation of the nucleus-vacuole junction (NVJ) is mediated by direct interaction between the vacuolar protein Vac8p and the outer nuclear endoplasmic reticulum membrane protein Nvj1p. Herein we report the crystal structure of Vac8p bound to Nvj1p at 2.4-A resolution. Vac8p comprises a flexibly connected N-terminal H1 helix followed by 12 armadillo repeats (ARMs) that form a right-handed superhelical structure. The extended 80-A-long loop of Nvj1p specifically binds the highly conserved inner groove formed from ARM1-12 of Vac8p. Disruption of the Nvj1p-Vac8p interaction results in the loss of tight NVJs, which impairs piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae Vac8p cationic triad (Arg276, Arg317, and Arg359) motifs interacting with Nvj1p are also critical to the recognition of Atg13p, a key component of the cytoplasm-to-vacuole targeting (CVT) pathway, indicating competitive binding to Vac8p. Indeed, mutation of the cationic triad abolishes CVT of Ape1p in vivo. Combined with biochemical data, the crystal structure reveals a Vac8p homodimer formed from ARM1, and this self-association, likely regulated by the flexible H1 helix and the C terminus of Nvj1p, is critical for Vac8p cellular functions.	+
-		+
-	Mechanistic insight into the nucleus-vacuole junction based on the Vac8p-Nvj1p crystal structure.,Jeong H, Park J, Kim HI, Lee M, Ko YJ, Lee S, Jun Y, Lee C Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4539-E4548. doi:, 10.1073/pnas.1701030114. Epub 2017 May 22. PMID:28533415<ref>PMID:28533415</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5xjg" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Baker's yeast~~]]	+	[[Category: Large Structures]]
-	[[Category: Jeong, H]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Jun, Y]]	+	[[Category: Jeong H]]
-	[[Category: Lee, C]]	+	[[Category: Jun Y]]
-	[[Category: Park, J]]	+	[[Category: Lee C]]
-	~~[[Category: Membrane contact site]]~~	+	[[Category: Park J]]
-	~~[[Category: Nucleus-vacuole junction]]~~	+
-	~~[[Category: Nvj1p]]~~	+
-	~~[[Category: Signaling protein-membrane protein complex]]~~	+
-	~~[[Category: Vac8p~~]]	+

OCA at 11:06, 16 November 2017

OCA — Thu, 16 Nov 2017 11:06:04 GMT

←Older revision		Revision as of 11:06, 16 November 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xjg is ~~ON HOLD~~	+	==Crystal structure of Vac8p bound to Nvj1p==
		+	<StructureSection load='5xjg' size='340' side='right' caption='[[5xjg]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5xjg]] 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=5XJG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XJG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B3P:2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>B3P</scene>, <scene name='pdbligand=PE5:3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL'>PE5</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">VAC8, YEB3, YEL013W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), NVJ1, VAB36, YHR195W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5xjg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xjg OCA], [http://pdbe.org/5xjg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xjg RCSB], [http://www.ebi.ac.uk/pdbsum/5xjg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xjg ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VAC8_YEAST VAC8_YEAST]] Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.<ref>PMID:9490720</ref> [[http://www.uniprot.org/uniprot/NVJ1_YEAST NVJ1_YEAST]] Involved in the formation of nucleus-vacuole (NV) junctions during piecemeal microautophagy of the nucleus (PMN). NV junctions are interorganelle interfaces mediated by NVJ1 in the nuclear envelope and VAC8 on the vacuole membrane. Together, NVJ1 and VAC8 form Velcro-like patches through which teardrop-like portions of the nucleus are pinched off into the vacuolar lumen and degraded by the PMN process. Acts also as an outer-nuclear membrane receptor for OSH1 and TSC13.<ref>PMID:10888680</ref> <ref>PMID:12529432</ref> <ref>PMID:15367582</ref> <ref>PMID:15958487</ref> <ref>PMID:16912077</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Formation of the nucleus-vacuole junction (NVJ) is mediated by direct interaction between the vacuolar protein Vac8p and the outer nuclear endoplasmic reticulum membrane protein Nvj1p. Herein we report the crystal structure of Vac8p bound to Nvj1p at 2.4-A resolution. Vac8p comprises a flexibly connected N-terminal H1 helix followed by 12 armadillo repeats (ARMs) that form a right-handed superhelical structure. The extended 80-A-long loop of Nvj1p specifically binds the highly conserved inner groove formed from ARM1-12 of Vac8p. Disruption of the Nvj1p-Vac8p interaction results in the loss of tight NVJs, which impairs piecemeal microautophagy of the nucleus in Saccharomyces cerevisiae Vac8p cationic triad (Arg276, Arg317, and Arg359) motifs interacting with Nvj1p are also critical to the recognition of Atg13p, a key component of the cytoplasm-to-vacuole targeting (CVT) pathway, indicating competitive binding to Vac8p. Indeed, mutation of the cationic triad abolishes CVT of Ape1p in vivo. Combined with biochemical data, the crystal structure reveals a Vac8p homodimer formed from ARM1, and this self-association, likely regulated by the flexible H1 helix and the C terminus of Nvj1p, is critical for Vac8p cellular functions.

-	~~Authors: Jeong~~, H., Park, J., ~~Jun~~, Y., Lee, C.	+	Mechanistic insight into the nucleus-vacuole junction based on the Vac8p-Nvj1p crystal structure.,Jeong H, Park J, Kim HI, Lee M, Ko YJ, Lee S, Jun Y, Lee C Proc Natl Acad Sci U S A. 2017 Jun 6;114(23):E4539-E4548. doi:, 10.1073/pnas.1701030114. Epub 2017 May 22. PMID:28533415<ref>PMID:28533415</ref>

-	~~Description: Crystal structure~~ of ~~Vac8p bound to Nvj1p~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5xjg" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Jeong, H]]		[[Category: Jeong, H]]
-	[[Category: Lee, C]]
	[[Category: Jun, Y]]		[[Category: Jun, Y]]
		+	[[Category: Lee, C]]
	[[Category: Park, J]]		[[Category: Park, J]]
		+	[[Category: Membrane contact site]]
		+	[[Category: Nucleus-vacuole junction]]
		+	[[Category: Nvj1p]]
		+	[[Category: Signaling protein-membrane protein complex]]
		+	[[Category: Vac8p]]

OCA at 14:52, 17 May 2017

OCA — Wed, 17 May 2017 14:52:10 GMT

←Older revision		Revision as of 14:52, 17 May 2017
Line 3:		Line 3:
	The entry 5xjg is ON HOLD		The entry 5xjg is ON HOLD

-	Authors: Jeong, H, Park, J, Jun, Y, Lee, C	+	Authors: Jeong, H., Park, J., Jun, Y., Lee, C.

	Description: Crystal structure of Vac8p bound to Nvj1p		Description: Crystal structure of Vac8p bound to Nvj1p
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Jeong, H, ~~Park, J,~~ Jun, Y, ~~Lee, C~~]]	+	[[Category: Jeong, H]]
		+	[[Category: Lee, C]]
		+	[[Category: Jun, Y]]
		+	[[Category: Park, J]]

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

OCA — Wed, 10 May 2017 12:01:32 GMT

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

←Older revision

Revision as of 12:01, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5xjg is ON HOLD Authors: Jeong, H, Park, J, Jun, Y, Lee, C Description: Crystal structure of Vac8p bound to Nvj1p [[Category: Unreleased Structures...

OCA — Wed, 10 May 2017 12:01:31 GMT

New page: '''Unreleased structure''' The entry 5xjg is ON HOLD Authors: Jeong, H, Park, J, Jun, Y, Lee, C Description: Crystal structure of Vac8p bound to Nvj1p [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 5xjg is ON HOLD

Authors: Jeong, H, Park, J, Jun, Y, Lee, C

Description: Crystal structure of Vac8p bound to Nvj1p
[[Category: Unreleased Structures]]
[[Category: Jeong, H, Park, J, Jun, Y, Lee, C]]