5ms5 - Revision history

OCA at 17:47, 8 November 2023

2023-11-08T17:47:55Z

←Older revision		Revision as of 17:47, 8 November 2023
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	<StructureSection load='5ms5' size='340' side='right'caption='[[5ms5]], [[Resolution\|resolution]] 1.53Å' scene=''>		<StructureSection load='5ms5' size='340' side='right'caption='[[5ms5]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ms5]] 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=5MS5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5MS5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ms5]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Legionella_pneumophila Legionella pneumophila]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MS5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MS5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.53Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~MAP1LC3B, MAP1ALC3 ([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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [~~http~~://pdbe.org/5ms5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 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=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [https://pdbe.org/5ms5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [https://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RAVZ_LEGPH RAVZ_LEGPH] Cysteine protease effector that inhibits host cell autophagy by targeting lipid-conjugated ATG8 family proteins on pre-autophagosomal structures (PubMed:23112293, PubMed:29458288, PubMed:32686895, PubMed:31722778, PubMed:31719622, PubMed:33298241, PubMed:26343456, PubMed:28395732). Specifically hydrolyzes the amide bond between the C-terminal glycine residue and an adjacent aromatic residue in ATG8 proteins conjugated to phosphatidylethanolamine (PE), producing an ATG8 protein that cannot be reconjugated by host ATG7 and ATG3 (PubMed:23112293, PubMed:29458288, PubMed:32686895, PubMed:26343456, PubMed:28395732). Mechanistically, Ravz interacts with ATG8 proteins conjugated to PE via its LIR motifs, extracts them from the membrane of autophagosomes and integrates the PE part into its own lipid-binding site (PubMed:28395732). It then removes the lipid component of the ATG8 protein (PubMed:28395732). Also able to mediate delipidation of ATG8 proteins conjugated to phosphatidylserine (PS) during non-canonical autophagy (PubMed:33909989). Inhibits host ubiquitin recruitment to bacteria-containing vacuoles, suggesting that it is able to mediate delipidation of other proteins in addition to ATG8 proteins (PubMed:28971069). It is however not involved in the exclusion of autophagy adapters from bacteria-containing vacuoles decorated with ubiquitin (PubMed:32482642).<ref>PMID:23112293</ref> <ref>PMID:26343456</ref> <ref>PMID:28395732</ref> <ref>PMID:28971069</ref> <ref>PMID:29458288</ref> <ref>PMID:31719622</ref> <ref>PMID:31722778</ref> <ref>PMID:32482642</ref> <ref>PMID:32686895</ref> <ref>PMID:33298241</ref> <ref>PMID:33909989</ref> [https://www.uniprot.org/uniprot/MLP3B_HUMAN MLP3B_HUMAN] Involved in formation of autophagosomal vacuoles (autophagosomes).
	<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: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pantoom, S~~]]	+	[[Category: Legionella pneumophila]]
-	[[Category: ~~Vetter, I R~~]]	+	[[Category: Pantoom S]]
-	[[Category: ~~Wu, Y W~~]]	+	[[Category: Vetter IR]]
-	[[Category: ~~Autophagy / host-pathogen interaction / protein binding /ravz / lir / lc3]]~~	+	[[Category: Wu YW]]
-	~~[[Category: Protein binding~~]]	+

OCA at 07:27, 19 August 2020

2020-08-19T07:27:38Z

←Older revision		Revision as of 07:27, 19 August 2020
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	==Low-salt structure of RavZ LIR2-fused human LC3B==		==Low-salt structure of RavZ LIR2-fused human LC3B==
-	<StructureSection load='5ms5' size='340' side='right' caption='[[5ms5]], [[Resolution\|resolution]] 1.53Å' scene=''>	+	<StructureSection load='5ms5' size='340' side='right'caption='[[5ms5]], [[Resolution\|resolution]] 1.53Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ms5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MS5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5MS5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ms5]] 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=5MS5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5MS5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [http://pdbe.org/5ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAP1LC3B, MAP1ALC3 ([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://proteopedia.org/fgij/fg.htm?mol=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [http://pdbe.org/5ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</div>		</div>
	<div class="pdbe-citations 5ms5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ms5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Microtubule-associated protein 3D structures\|Microtubule-associated protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Pantoom, S]]		[[Category: Pantoom, S]]
	[[Category: Vetter, I R]]		[[Category: Vetter, I R]]

OCA at 07:34, 27 April 2017

2017-04-27T07:34:27Z

←Older revision		Revision as of 07:34, 27 April 2017
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	<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=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [http://pdbe.org/5ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 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=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [http://pdbe.org/5ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Autophagy is a conserved cellular process involved in the elimination of proteins and organelles. It is also used to combat infection with pathogenic microbes. The intracellular pathogen Legionella pneumophila manipulates autophagy by delivering the effector protein RavZ to deconjugate Atg8/LC3 proteins coupled to phosphatidylethanolamine (PE) on autophagosomal membranes. To understand how RavZ recognizes and deconjugates LC3-PE, we prepared semisynthetic LC3 proteins and elucidated the structures of the RavZ:LC3 interaction. Semisynthetic LC3 proteins allowed the analysis of structure-function relationships. RavZ extracts LC3-PE from the membrane before deconjugation. RavZ initially recognizes the LC3 molecule on membranes via its N-terminal LC3-interacting region (LIR) motif. The RavZ alpha3 helix is involved in extraction of the PE moiety and docking of the acyl chains into the lipid-binding site of RavZ that is related in structure to that of the phospholipid transfer protein Sec14. Thus, Legionella has evolved a novel mechanism to specifically evade host autophagy.
		+
		+	Elucidation of the anti-autophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins.,Yang A, Pantoom S, Wu YW Elife. 2017 Apr 11;6. pii: e23905. doi: 10.7554/eLife.23905. PMID:28395732<ref>PMID:28395732</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ms5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 13:01, 19 April 2017

2017-04-19T13:01:16Z

←Older revision		Revision as of 13:01, 19 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ms5 ~~is ON HOLD until Paper Publication~~	+	==Low-salt structure of RavZ LIR2-fused human LC3B==
-		+	<StructureSection load='5ms5' size='340' side='right' caption='[[5ms5]], [[Resolution\|resolution]] 1.53Å' scene=''>
-	~~Authors~~: ~~Pantoom, S~~.~~, Vetter, I~~.R.~~, Wu, Y~~.W.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5ms5]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MS5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MS5 FirstGlance]. <br>
-	~~Description~~: ~~Low~~-~~salt structure of RavZ LIR2~~-~~fused human LC3B~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ms5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ms5 OCA], [http://pdbe.org/5ms5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ms5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ms5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ms5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Pantoom, S]]		[[Category: Pantoom, S]]
-	[[Category: Vetter, I.R]]	+	[[Category: Vetter, I R]]
-	[[Category: Wu, Y.W]]	+	[[Category: Wu, Y W]]
		+	[[Category: Autophagy / host-pathogen interaction / protein binding /ravz / lir / lc3]]
		+	[[Category: Protein binding]]

OCA: Protected "5ms5" [edit=sysop:move=sysop]

2017-01-18T13:08:49Z

Protected "5ms5" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:08, 18 January 2017

OCA: New page: '''Unreleased structure''' The entry 5ms5 is ON HOLD until Paper Publication Authors: Pantoom, S., Vetter, I.R., Wu, Y.W. Description: Low-salt structure of RavZ LIR2-fused human LC3B ...

2017-01-18T13:08:48Z

New page: '''Unreleased structure''' The entry 5ms5 is ON HOLD until Paper Publication Authors: Pantoom, S., Vetter, I.R., Wu, Y.W. Description: Low-salt structure of RavZ LIR2-fused human LC3B ...

New page

'''Unreleased structure'''

The entry 5ms5 is ON HOLD until Paper Publication

Authors: Pantoom, S., Vetter, I.R., Wu, Y.W.

Description: Low-salt structure of RavZ LIR2-fused human LC3B
[[Category: Unreleased Structures]]
[[Category: Pantoom, S]]
[[Category: Vetter, I.R]]
[[Category: Wu, Y.W]]