5yir - Revision history

OCA at 08:31, 22 November 2023

OCA — Wed, 22 Nov 2023 08:31:13 GMT

←Older revision		Revision as of 08:31, 22 November 2023
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	==Crystal Structure of AnkB LIR/GABARAP complex==		==Crystal Structure of AnkB LIR/GABARAP complex==
-	<StructureSection load='5yir' size='340' side='right' caption='[[5yir]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='5yir' size='340' side='right'caption='[[5yir]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yir]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YIR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yir]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YIR FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=NI:NICKEL+(II)+ION'>NI</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]] 2.75Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Gabarap ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10090 LK3 transgenic mice]~~)~~, ANK2 ([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=NI:NICKEL+(II)+ION'>NI</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=5yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yir OCA], [~~http~~://pdbe.org/5yir PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yir RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yir PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yir 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=5yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yir OCA], [https://pdbe.org/5yir PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yir RCSB], [https://www.ebi.ac.uk/pdbsum/5yir PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yir ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] Romano-Ward syndrome. Long QT syndrome 4 (LQT4) [MIM:[http://omim.org/entry/600919 600919]]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. Long QT syndrome type 4 shows many atypical features compared to classical long QT syndromes, including pronounced sinus bradycardia, polyphasic T waves and atrial fibrillation. Cardiac repolarization defects may be not as severe as in classical LQT syndromes and prolonged QT interval on EKG is not a consistent feature. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:12571597</ref> <ref>PMID:15178757</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GBRAP_MOUSE GBRAP_MOUSE]] Ubiquitin-like modifier that plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). [[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions (By similarity). Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors. Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate.<ref>PMID:12571597</ref>	+	[https://www.uniprot.org/uniprot/GBRAP_MOUSE GBRAP_MOUSE] Ubiquitin-like modifier that plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5yir" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5yir" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[GABA receptor-associated protein 3D structures\|GABA receptor-associated protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: Chen, K]]	+	[[Category: Mus musculus]]
-	[[Category: Li, J]]	+	[[Category: Chen K]]
-	[[Category: Wang, C]]	+	[[Category: Li J]]
-	[[Category: Yuan, C]]	+	[[Category: Wang C]]
-	[[Category: Zhang, H]]	+	[[Category: Yuan C]]
-	[[Category: Zhang, M]]	+	[[Category: Zhang H]]
-	[[Category: Zheng, H]]	+	[[Category: Zhang M]]
-	[[Category: Zhu, R]]	+	[[Category: Zheng H]]
-	~~[[Category: Autophagy]]~~	+	[[Category: Zhu R]]
-	~~[[Category: Protein binding~~]]	+

OCA at 07:36, 4 July 2018

OCA — Wed, 04 Jul 2018 07:36:16 GMT

←Older revision		Revision as of 07:36, 4 July 2018
Line 3:		Line 3:
	<StructureSection load='5yir' size='340' side='right' caption='[[5yir]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='5yir' size='340' side='right' caption='[[5yir]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yir]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yir]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIR FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Gabarap ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice]), ANK2 ([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=5yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yir OCA], [http://pdbe.org/5yir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yir RCSB], [http://www.ebi.ac.uk/pdbsum/5yir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yir 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=5yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yir OCA], [http://pdbe.org/5yir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yir RCSB], [http://www.ebi.ac.uk/pdbsum/5yir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yir ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/GBRAP_MOUSE GBRAP_MOUSE]] Ubiquitin-like modifier that plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). [[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions (By similarity). Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors. Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate.<ref>PMID:12571597</ref>		[[http://www.uniprot.org/uniprot/GBRAP_MOUSE GBRAP_MOUSE]] Ubiquitin-like modifier that plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). [[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions (By similarity). Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors. Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate.<ref>PMID:12571597</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The mammalian Atg8 family proteins are central drivers of autophagy and contain six members, classified into the LC3 and GABARAP subfamilies. Due to their high sequence similarity and consequent functional overlaps, it is difficult to delineate specific functions of Atg8 proteins in autophagy. Here we discover a super-strong GABARAP-selective inhibitory peptide harbored in 270/480 kDa ankyrin-G and a super-potent pan-Atg8 inhibitory peptide from 440 kDa ankyrin-B. Structural studies elucidate the mechanism governing the Atg8 binding potency and selectivity of the peptides, reveal a general Atg8-binding sequence motif, and allow development of a more GABARAP-selective inhibitory peptide. These peptides effectively blocked autophagy when expressed in cultured cells. Expression of these ankyrin-derived peptides in Caenorhabditis elegans also inhibited autophagy, causing accumulation of the p62 homolog SQST-1, delayed development and shortened life span. Thus, these genetically encodable autophagy inhibitory peptides can be used to occlude autophagy spatiotemporally in living animals.
		+
		+	Potent and specific Atg8-targeting autophagy inhibitory peptides from giant ankyrins.,Li J, Zhu R, Chen K, Zheng H, Zhao H, Yuan C, Zhang H, Wang C, Zhang M Nat Chem Biol. 2018 Jun 4. pii: 10.1038/s41589-018-0082-8. doi:, 10.1038/s41589-018-0082-8. PMID:29867141<ref>PMID:29867141</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yir" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Chen, K]]		[[Category: Chen, K]]
	[[Category: Li, J]]		[[Category: Li, J]]

OCA at 07:17, 23 May 2018

OCA — Wed, 23 May 2018 07:17:55 GMT

←Older revision		Revision as of 07:17, 23 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	The entry ~~5yir~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal Structure of AnkB LIR/GABARAP complex==
-		+	<StructureSection load='5yir' size='340' side='right' caption='[[5yir]], [[Resolution\|resolution]] 2.75Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yir]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YIR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YIR FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5yir FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yir OCA], [http://pdbe.org/5yir PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yir RCSB], [http://www.ebi.ac.uk/pdbsum/5yir PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yir ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] Romano-Ward syndrome. Long QT syndrome 4 (LQT4) [MIM:[http://omim.org/entry/600919 600919]]: A heart disorder characterized by a prolonged QT interval on the ECG and polymorphic ventricular arrhythmias. They cause syncope and sudden death in response to exercise or emotional stress, and can present with a sentinel event of sudden cardiac death in infancy. Long QT syndrome type 4 shows many atypical features compared to classical long QT syndromes, including pronounced sinus bradycardia, polyphasic T waves and atrial fibrillation. Cardiac repolarization defects may be not as severe as in classical LQT syndromes and prolonged QT interval on EKG is not a consistent feature. Note=The disease is caused by mutations affecting the gene represented in this entry.<ref>PMID:12571597</ref> <ref>PMID:15178757</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GBRAP_MOUSE GBRAP_MOUSE]] Ubiquitin-like modifier that plays a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy. Whereas LC3s are involved in elongation of the phagophore membrane, the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation (By similarity). [[http://www.uniprot.org/uniprot/ANK2_HUMAN ANK2_HUMAN]] In skeletal muscle, required for proper localization of DMD and DCTN4 and for the formation and/or stability of a special subset of microtubules associated with costameres and neuromuscular junctions (By similarity). Attaches integral membrane proteins to cytoskeletal elements. Also binds to cytoskeletal proteins. Required for coordinate assembly of Na/Ca exchanger, Na/K ATPase and InsP3 receptor at sarcoplasmic reticulum sites in cardiomyocytes. Required for the coordinated expression of the Na/K ATPase, Na/Ca exchanger and beta-2-spectrin (SPTBN1) in the inner segment of rod photoreceptors. Required for expression and targeting of SPTBN1 in neonatal cardiomyocytes and for the regulation of neonatal cardiomyocyte contraction rate.<ref>PMID:12571597</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chen, K]]
		+	[[Category: Li, J]]
		+	[[Category: Wang, C]]
		+	[[Category: Yuan, C]]
		+	[[Category: Zhang, H]]
		+	[[Category: Zhang, M]]
		+	[[Category: Zheng, H]]
		+	[[Category: Zhu, R]]
		+	[[Category: Autophagy]]
		+	[[Category: Protein binding]]

OCA at 05:36, 25 October 2017

OCA — Wed, 25 Oct 2017 05:36:07 GMT

←Older revision		Revision as of 05:36, 25 October 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yir is ON HOLD	+	The entry 5yir is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 11 Oct 2017 05:25:38 GMT

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

←Older revision

Revision as of 05:25, 11 October 2017

OCA: New page: '''Unreleased structure''' The entry 5yir is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Oct 2017 05:25:37 GMT

New page: '''Unreleased structure''' The entry 5yir is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yir is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]