5ype - Revision history

OCA at 10:24, 27 March 2024

2024-03-27T10:24:40Z

←Older revision		Revision as of 10:24, 27 March 2024
Line 1:		Line 1:

	==p62/SQSTM1 ZZ domain with Tyr-peptide==		==p62/SQSTM1 ZZ domain with Tyr-peptide==
-	<StructureSection load='5ype' size='340' side='right' caption='[[5ype]], [[Resolution\|resolution]] 2.85Å' scene=''>	+	<StructureSection load='5ype' size='340' side='right'caption='[[5ype]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ype]] 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=5YPE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YPE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ype]] 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=5YPE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YPE 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]] 2.851Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SQSTM1, ORCA, OSIL ([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=ZN:ZINC+ION'>ZN</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=5ype FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ype OCA], [~~http~~://pdbe.org/5ype PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ype RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ype PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ype 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=5ype FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ype OCA], [https://pdbe.org/5ype PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ype RCSB], [https://www.ebi.ac.uk/pdbsum/5ype PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ype ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/~~GRP78_HUMAN GRP78_HUMAN~~]] Note=Autoantigen in rheumatoid arthritis.<ref>PMID:11160188</ref>	+	[https://www.uniprot.org/uniprot/SQSTM_HUMAN SQSTM_HUMAN] Defects in SQSTM1 are a cause of Paget disease of bone (PDB) [MIM:[https://omim.org/entry/602080 602080]. PDB is a metabolic bone disease affecting the axial skeleton and characterized by focal areas of increased and disorganized bone turn-over due to activated osteoclasts. Manifestations of the disease include bone pain, deformity, pathological fractures, deafness, neurological complications and increased risk of osteosarcoma. PDB is a chronic disease affecting 2 to 3% of the population above the age of 40 years.<ref>PMID:19931284</ref> <ref>PMID:11992264</ref> <ref>PMID:12374763</ref> <ref>PMID:14584883</ref> <ref>PMID:15146436</ref> <ref>PMID:15207768</ref> <ref>PMID:15125799</ref> <ref>PMID:15176995</ref> Note=In a cell model for Huntington disease (HD), appears to form a shell surrounding aggregates of mutant HTT that may protect cells from apoptosis, possibly by recruiting autophagosomal components to the polyubiquitinylated protein aggregates.<ref>PMID:16286508</ref> [https://www.uniprot.org/uniprot/BIP_HUMAN BIP_HUMAN] Autoantigen in rheumatoid arthritis.<ref>PMID:11160188</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~GRP78_HUMAN GRP78_HUMAN~~]~~] Probably plays~~ a role in ~~facilitating~~ the ~~assembly~~ of ~~multimeric protein complexes inside the ER~~.<ref>PMID:~~2294010~~</ref>	+	[https://www.uniprot.org/uniprot/SQSTM_HUMAN SQSTM_HUMAN] Required both for the formation and autophagic degradation of polyubiquitin-containing bodies, called ALIS (aggresome-like induced structures). Links ALIS to the autophagic machinery via direct interaction with MAP1 LC3 family members. May regulate the activation of NFKB1 by TNF-alpha, nerve growth factor (NGF) and interleukin-1. May play a role in titin/TTN downstream signaling in muscle cells. May regulate signaling cascades through ubiquitination. Adapter that mediates the interaction between TRAF6 and CYLD (By similarity). May be involved in cell differentiation, apoptosis, immune response and regulation of K(+) channels.<ref>PMID:10356400</ref> <ref>PMID:10747026</ref> <ref>PMID:11244088</ref> <ref>PMID:12471037</ref> <ref>PMID:15340068</ref> <ref>PMID:16079148</ref> <ref>PMID:16286508</ref> <ref>PMID:15953362</ref> <ref>PMID:15911346</ref> <ref>PMID:15802564</ref> <ref>PMID:19931284</ref> [https://www.uniprot.org/uniprot/BIP_HUMAN BIP_HUMAN] Endoplasmic reticulum chaperone that plays a key role in protein folding and quality control in the endoplasmic reticulum lumen (PubMed:2294010, PubMed:23769672, PubMed:23990668, PubMed:28332555). Involved in the correct folding of proteins and degradation of misfolded proteins via its interaction with DNAJC10/ERdj5, probably to facilitate the release of DNAJC10/ERdj5 from its substrate (By similarity). Acts as a key repressor of the ERN1/IRE1-mediated unfolded protein response (UPR) (PubMed:1550958, PubMed:19538957). In the unstressed endoplasmic reticulum, recruited by DNAJB9/ERdj4 to the luminal region of ERN1/IRE1, leading to disrupt the dimerization of ERN1/IRE1, thereby inactivating ERN1/IRE1 (By similarity). Accumulation of misfolded protein in the endoplasmic reticulum causes release of HSPA5/BiP from ERN1/IRE1, allowing homodimerization and subsequent activation of ERN1/IRE1 (By similarity). Plays an auxiliary role in post-translational transport of small presecretory proteins across endoplasmic reticulum (ER). May function as an allosteric modulator for SEC61 channel-forming translocon complex, likely cooperating with SEC62 to enable the productive insertion of these precursors into SEC61 channel. Appears to specifically regulate translocation of precursors having inhibitory residues in their mature region that weaken channel gating.[UniProtKB:G3I8R9][UniProtKB:P20029]<ref>PMID:1550958</ref> <ref>PMID:19538957</ref> <ref>PMID:2294010</ref> <ref>PMID:23769672</ref> <ref>PMID:23990668</ref> <ref>PMID:28332555</ref> <ref>PMID:29719251</ref>
-	<~~div style="background-color~~:~~#fffaf0;"~~>	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~p62~~/~~SQSTM1 is the~~ key ~~autophagy adapter~~ protein and the ~~hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However~~, the ~~exact recognition mode~~ of ~~degrading substrates~~ and ~~regulation~~ of ~~p62 in the autophagic pathway remain unknown. Here~~, ~~we present~~ the ~~complex structures between the ZZ-domain~~ of ~~p62 and various type-1 and type-2 N-degrons~~. ~~The binding mode employed in the interaction~~ of the ZZ-~~domain with N-degrons differs from that employed by classic N-recognins~~. ~~It was also determined that oligomerization via~~ the ~~PB1 domain can control functional affinity~~ to the ~~R-BiP substrate. Unexpectedly~~, ~~we found that self-oligomerization and disassembly~~ of ~~p62 are pH-dependent~~. ~~These findings broaden our understanding~~ of the ~~functional repertoire~~ of ~~the N-end rule pathway~~ and ~~provide an insight into the regulation~~ of ~~p62 during the autophagic pathway~~.	+
-		+
-	~~Insights into degradation mechanism~~ of N-~~end rule substrates by p62/SQSTM1 autophagy adapter.,Kwon DH, Park OH, Kim L, Jung YO, Park Y, Jeong H, Hyun J, Kim YK~~, ~~Song HK Nat Commun~~. ~~2018 Aug 17;9(1):3291~~. ~~doi~~: ~~10.1038~~/~~s41467-018-05825-x.~~ PMID:~~30120248~~<ref>PMID:~~30120248~~</ref>	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 5ype" style="background-color~~:~~#fffaf0;"~~></~~div~~>	+

	==See Also==		==See Also==
Line 28:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Kim, L~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Kwon, D H~~]]	+	[[Category: Kim L]]
-	[[Category: ~~Song, H K~~]]	+	[[Category: Kwon DH]]
-	[[Category: ~~Autophagy]]~~	+	[[Category: Song HK]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: N-end rule]]~~	+
-	~~[[Category: P62/sqstm1]]~~	+
-	~~[[Category: Signaling protein]]~~	+
-	~~[[Category: Zz domain~~]]	+

OCA at 08:35, 3 October 2018

2018-10-03T08:35:23Z

←Older revision		Revision as of 08:35, 3 October 2018
Line 1:		Line 1:

-	==~~Zinc binding protein complex~~ with Tyr-peptide==	+	==p62/SQSTM1 ZZ domain with Tyr-peptide==
	<StructureSection load='5ype' size='340' side='right' caption='[[5ype]], [[Resolution\|resolution]] 2.85Å' scene=''>		<StructureSection load='5ype' size='340' side='right' caption='[[5ype]], [[Resolution\|resolution]] 2.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ype]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ype]] 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=5YPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPE 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">SQSTM1, ORCA, OSIL ([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=5ype FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ype OCA], [http://pdbe.org/5ype PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ype RCSB], [http://www.ebi.ac.uk/pdbsum/5ype PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ype 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=5ype FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ype OCA], [http://pdbe.org/5ype PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ype RCSB], [http://www.ebi.ac.uk/pdbsum/5ype PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ype ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5ype" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ype" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sequestosome\|Sequestosome]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Kim, L]]		[[Category: Kim, L]]
	[[Category: Kwon, D H]]		[[Category: Kwon, D H]]

OCA at 07:19, 29 August 2018

2018-08-29T07:19:13Z

←Older revision		Revision as of 07:19, 29 August 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ype is ~~ON HOLD~~ ~~until Nov 01 2019~~	+	==Zinc binding protein complex with Tyr-peptide==
		+	<StructureSection load='5ype' size='340' side='right' caption='[[5ype]], [[Resolution\|resolution]] 2.85Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ype]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YPE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YPE 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='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=5ype FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ype OCA], [http://pdbe.org/5ype PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ype RCSB], [http://www.ebi.ac.uk/pdbsum/5ype PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ype ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/GRP78_HUMAN GRP78_HUMAN]] Note=Autoantigen in rheumatoid arthritis.<ref>PMID:11160188</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GRP78_HUMAN GRP78_HUMAN]] Probably plays a role in facilitating the assembly of multimeric protein complexes inside the ER.<ref>PMID:2294010</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	p62/SQSTM1 is the key autophagy adapter protein and the hub of multi-cellular signaling. It was recently reported that autophagy and N-end rule pathways are linked via p62. However, the exact recognition mode of degrading substrates and regulation of p62 in the autophagic pathway remain unknown. Here, we present the complex structures between the ZZ-domain of p62 and various type-1 and type-2 N-degrons. The binding mode employed in the interaction of the ZZ-domain with N-degrons differs from that employed by classic N-recognins. It was also determined that oligomerization via the PB1 domain can control functional affinity to the R-BiP substrate. Unexpectedly, we found that self-oligomerization and disassembly of p62 are pH-dependent. These findings broaden our understanding of the functional repertoire of the N-end rule pathway and provide an insight into the regulation of p62 during the autophagic pathway.

-	~~Authors:~~ Kwon, ~~D.H.~~, Kim, L., ~~Song~~, H.K.	+	Insights into degradation mechanism of N-end rule substrates by p62/SQSTM1 autophagy adapter.,Kwon DH, Park OH, Kim L, Jung YO, Park Y, Jeong H, Hyun J, Kim YK, Song HK Nat Commun. 2018 Aug 17;9(1):3291. doi: 10.1038/s41467-018-05825-x. PMID:30120248<ref>PMID:30120248</ref>

-	~~Description: Zinc binding protein complex with Tyr-peptide~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Kwon, D.H]]~~	+	<div class="pdbe-citations 5ype" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Kim, L]]		[[Category: Kim, L]]
-	[[Category: Song, H.K]]	+	[[Category: Kwon, D H]]
		+	[[Category: Song, H K]]
		+	[[Category: Autophagy]]
		+	[[Category: Complex]]
		+	[[Category: N-end rule]]
		+	[[Category: P62/sqstm1]]
		+	[[Category: Signaling protein]]
		+	[[Category: Zz domain]]

OCA at 07:10, 27 December 2017

2017-12-27T07:10:22Z

←Older revision		Revision as of 07:10, 27 December 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ype is ON HOLD	+	The entry 5ype is ON HOLD until Nov 01 2019

	Authors: Kwon, D.H., Kim, L., Song, H.K.		Authors: Kwon, D.H., Kim, L., Song, H.K.

OCA at 05:45, 13 December 2017

2017-12-13T05:45:50Z

←Older revision		Revision as of 05:45, 13 December 2017
Line 5:		Line 5:
	Authors: Kwon, D.H., Kim, L., Song, H.K.		Authors: Kwon, D.H., Kim, L., Song, H.K.

-	Description: Zinc binding protein ~~complexed~~ with ~~Arg~~-peptide	+	Description: Zinc binding protein complex with Tyr-peptide
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Kwon, D.H]]		[[Category: Kwon, D.H]]
	[[Category: Kim, L]]		[[Category: Kim, L]]
	[[Category: Song, H.K]]		[[Category: Song, H.K]]

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

2017-11-08T06:28:47Z

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

←Older revision

Revision as of 06:28, 8 November 2017

OCA: New page: '''Unreleased structure''' The entry 5ype is ON HOLD Authors: Kwon, D.H., Kim, L., Song, H.K. Description: Zinc binding protein complexed with Arg-peptide [[Category: Unreleased Struct...

2017-11-08T06:28:46Z

New page: '''Unreleased structure''' The entry 5ype is ON HOLD Authors: Kwon, D.H., Kim, L., Song, H.K. Description: Zinc binding protein complexed with Arg-peptide [[Category: Unreleased Struct...

New page

'''Unreleased structure'''

The entry 5ype is ON HOLD

Authors: Kwon, D.H., Kim, L., Song, H.K.

Description: Zinc binding protein complexed with Arg-peptide
[[Category: Unreleased Structures]]
[[Category: Kwon, D.H]]
[[Category: Kim, L]]
[[Category: Song, H.K]]