6hym - Revision history

OCA at 11:42, 24 January 2024

OCA — Wed, 24 Jan 2024 11:42:34 GMT

←Older revision		Revision as of 11:42, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6hym' size='340' side='right'caption='[[6hym]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6hym' size='340' side='right'caption='[[6hym]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hym]] is a 2 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=6HYM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hym]] is a 2 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=6HYM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HYM FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1,2~~-~~ETHANEDIOL'>EDO</scene>~~, ~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.86Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~GABARAP, FLC3B, HT004 ([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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6hym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hym OCA], [~~http~~://pdbe.org/6hym PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6hym RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6hym PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6hym 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=6hym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hym OCA], [https://pdbe.org/6hym PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hym RCSB], [https://www.ebi.ac.uk/pdbsum/6hym PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hym ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Differentiated thyroid carcinoma. A chromosomal aberration involving PCM1 is found in papillary thyroid carcinomas (PTCs) (PubMed:10980597). Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1 (PubMed:10980597).<ref>PMID:10980597</ref> A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865). Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1 (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865).<ref>PMID:15805263</ref> <ref>PMID:16034466</ref> <ref>PMID:16091753</ref> <ref>PMID:16424865</ref> <ref>PMID:16769584</ref>	+	[https://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN] Differentiated thyroid carcinoma. A chromosomal aberration involving PCM1 is found in papillary thyroid carcinomas (PTCs) (PubMed:10980597). Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1 (PubMed:10980597).<ref>PMID:10980597</ref> A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865). Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1 (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865).<ref>PMID:15805263</ref> <ref>PMID:16034466</ref> <ref>PMID:16091753</ref> <ref>PMID:16424865</ref> <ref>PMID:16769584</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310).<ref>PMID:12403812</ref> <ref>PMID:15659651</ref> <ref>PMID:16943179</ref> <ref>PMID:20551181</ref> <ref>PMID:24121310</ref>	+	[https://www.uniprot.org/uniprot/GBRAP_HUMAN GBRAP_HUMAN] May play a role in intracellular transport of GABA(A) receptors and its interaction with the cytoskeleton. Involved in apoptosis. Involved in autophagy (By similarity).<ref>PMID:15977068</ref> [https://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN] Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310).<ref>PMID:12403812</ref> <ref>PMID:15659651</ref> <ref>PMID:16943179</ref> <ref>PMID:20551181</ref> <ref>PMID:24121310</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 6hym" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6hym" 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: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Johansen, T]]	+	[[Category: Johansen T]]
-	[[Category: Joshi, D]]	+	[[Category: Joshi D]]
-	[[Category: Mouilleron, S]]	+	[[Category: Mouilleron S]]
-	[[Category: Nyoni, L]]	+	[[Category: Nyoni L]]
-	[[Category: ~~Razi, M~~]]	+	[[Category: O'Reilly N]]
-	[[Category: ~~Reilly, N O~~]]	+	[[Category: Razi M]]
-	[[Category: Tooze, S]]	+	[[Category: Tooze S]]
-	[[Category: Wirth, M]]	+	[[Category: Wirth M]]
-	[[Category: Zhang, W]]	+	[[Category: Zhang W]]
-	~~[[Category: Atg8]]~~	+
-	~~[[Category: Autophagy]]~~	+
-	~~[[Category: Lir]]~~	+
-	~~[[Category: Signaling protein~~]]	+

OCA at 08:14, 21 May 2019

OCA — Tue, 21 May 2019 08:14:50 GMT

←Older revision		Revision as of 08:14, 21 May 2019
Line 3:		Line 3:
	<StructureSection load='6hym' size='340' side='right'caption='[[6hym]], [[Resolution\|resolution]] 1.86Å' scene=''>		<StructureSection load='6hym' size='340' side='right'caption='[[6hym]], [[Resolution\|resolution]] 1.86Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hym]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HYM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hym]] is a 2 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=6HYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HYM FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GABARAP, FLC3B, HT004 ([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=6hym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hym OCA], [http://pdbe.org/6hym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hym RCSB], [http://www.ebi.ac.uk/pdbsum/6hym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hym 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=6hym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hym OCA], [http://pdbe.org/6hym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hym RCSB], [http://www.ebi.ac.uk/pdbsum/6hym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hym ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310).<ref>PMID:12403812</ref> <ref>PMID:15659651</ref> <ref>PMID:16943179</ref> <ref>PMID:20551181</ref> <ref>PMID:24121310</ref>		[[http://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310).<ref>PMID:12403812</ref> <ref>PMID:15659651</ref> <ref>PMID:16943179</ref> <ref>PMID:20551181</ref> <ref>PMID:24121310</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Autophagy is an essential recycling and quality control pathway. Mammalian ATG8 proteins drive autophagosome formation and selective removal of protein aggregates and organelles by recruiting autophagy receptors and adaptors that contain a LC3-interacting region (LIR) motif. LIR motifs can be highly selective for ATG8 subfamily proteins (LC3s/GABARAPs), however the molecular determinants regulating these selective interactions remain elusive. Here we show that residues within the core LIR motif and adjacent C-terminal region as well as ATG8 subfamily-specific residues in the LIR docking site are critical for binding of receptors and adaptors to GABARAPs. Moreover, rendering GABARAP more LC3B-like impairs autophagy receptor degradation. Modulating LIR binding specificity of the centriolar satellite protein PCM1, implicated in autophagy and centrosomal function, alters its dynamics in cells. Our data provides new mechanistic insight into how selective binding of LIR motifs to GABARAPs is achieved, and elucidate the overlapping and distinct functions of ATG8 subfamily proteins.
		+
		+	Molecular determinants regulating selective binding of autophagy adapters and receptors to ATG8 proteins.,Wirth M, Zhang W, Razi M, Nyoni L, Joshi D, O'Reilly N, Johansen T, Tooze SA, Mouilleron S Nat Commun. 2019 May 3;10(1):2055. doi: 10.1038/s41467-019-10059-6. PMID:31053714<ref>PMID:31053714</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6hym" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Johansen, T]]		[[Category: Johansen, T]]

OCA at 11:19, 10 May 2019

OCA — Fri, 10 May 2019 11:19:05 GMT

←Older revision		Revision as of 11:19, 10 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6hym is ~~ON HOLD~~	+	==Structure of PCM1 LIR motif bound to GABARAP==
-		+	<StructureSection load='6hym' size='340' side='right'caption='[[6hym]], [[Resolution\|resolution]] 1.86Å' scene=''>
-	~~Authors~~: ~~Mouilleron~~, S., ~~Wirth~~, M., ~~Zhang~~, W., ~~O'Reilly~~, N., ~~Tooze~~, S., ~~Johansen~~, T., ~~Razi~~, M., ~~Nyoni~~, L., ~~Joshi~~, D.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6hym]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HYM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HYM FirstGlance]. <br>
-	~~Description: Structure of PCM1 LIR motif bound to GABARAP~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=6hym FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hym OCA], [http://pdbe.org/6hym PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hym RCSB], [http://www.ebi.ac.uk/pdbsum/6hym PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hym ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Differentiated thyroid carcinoma. A chromosomal aberration involving PCM1 is found in papillary thyroid carcinomas (PTCs) (PubMed:10980597). Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1 (PubMed:10980597).<ref>PMID:10980597</ref> A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865). Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1 (PubMed:15805263, PubMed:16034466, PubMed:16091753, PubMed:16769584, PubMed:16424865).<ref>PMID:15805263</ref> <ref>PMID:16034466</ref> <ref>PMID:16091753</ref> <ref>PMID:16424865</ref> <ref>PMID:16769584</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCM1_HUMAN PCM1_HUMAN]] Required for centrosome assembly and function (PubMed:12403812, PubMed:15659651, PubMed:16943179). Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2 (PubMed:12403812, PubMed:15659651). Required to anchor microtubules to the centrosome (PubMed:12403812, PubMed:15659651). Involved in the biogenesis of cilia (PubMed:20551181, PubMed:24121310).<ref>PMID:12403812</ref> <ref>PMID:15659651</ref> <ref>PMID:16943179</ref> <ref>PMID:20551181</ref> <ref>PMID:24121310</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Johansen, T]]
	[[Category: Joshi, D]]		[[Category: Joshi, D]]
		+	[[Category: Mouilleron, S]]
		+	[[Category: Nyoni, L]]
	[[Category: Razi, M]]		[[Category: Razi, M]]
-	[[Category: ~~Johansen, T]]~~	+	[[Category: Reilly, N O]]
-	~~[[Category: Zhang, W]]~~	+
-	~~[[Category: Nyoni, L]]~~	+
-	~~[[Category: O'~~Reilly, N]]	+
	[[Category: Tooze, S]]		[[Category: Tooze, S]]
-	[[Category: Mouilleron, S]]
	[[Category: Wirth, M]]		[[Category: Wirth, M]]
		+	[[Category: Zhang, W]]
		+	[[Category: Atg8]]
		+	[[Category: Autophagy]]
		+	[[Category: Lir]]
		+	[[Category: Signaling protein]]

OCA: Protected "6hym" [edit=sysop:move=sysop]

OCA — Wed, 31 Oct 2018 05:11:31 GMT

Protected "6hym" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:11, 31 October 2018

OCA: New page: '''Unreleased structure''' The entry 6hym is ON HOLD Authors: Mouilleron, S., Wirth, M., Zhang, W., O'Reilly, N., Tooze, S., Johansen, T., Razi, M., Nyoni, L., Joshi, D. Description: S...

OCA — Wed, 31 Oct 2018 05:11:30 GMT

New page: '''Unreleased structure''' The entry 6hym is ON HOLD Authors: Mouilleron, S., Wirth, M., Zhang, W., O'Reilly, N., Tooze, S., Johansen, T., Razi, M., Nyoni, L., Joshi, D. Description: S...

New page

'''Unreleased structure'''

The entry 6hym is ON HOLD

Authors: Mouilleron, S., Wirth, M., Zhang, W., O'Reilly, N., Tooze, S., Johansen, T., Razi, M., Nyoni, L., Joshi, D.

Description: Structure of PCM1 LIR motif bound to GABARAP
[[Category: Unreleased Structures]]
[[Category: Joshi, D]]
[[Category: Razi, M]]
[[Category: Johansen, T]]
[[Category: Zhang, W]]
[[Category: Nyoni, L]]
[[Category: O'Reilly, N]]
[[Category: Tooze, S]]
[[Category: Mouilleron, S]]
[[Category: Wirth, M]]