5zm6 - Revision history

OCA at 09:00, 22 November 2023

OCA — Wed, 22 Nov 2023 09:00:52 GMT

←Older revision		Revision as of 09:00, 22 November 2023
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	==Crystal structure of ORP1-ORD in complex with PI(4,5)P2==		==Crystal structure of ORP1-ORD in complex with PI(4,5)P2==
-	<StructureSection load='5zm6' size='340' side='right' caption='[[5zm6]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5zm6' size='340' side='right'caption='[[5zm6]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zm6]] 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=5ZM6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZM6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zm6]] 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=5ZM6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZM6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IEP:[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl]+icosa-5,8,11,14-tetraenoate'>IEP</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]] 2.7Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OSBPL1A, ORP1, OSBP8, OSBPL1, OSBPL1B ([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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IEP:[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl]+icosa-5,8,11,14-tetraenoate'>IEP</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=5zm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm6 OCA], [~~http~~://pdbe.org/5zm6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zm6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zm6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm6 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=5zm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm6 OCA], [https://pdbe.org/5zm6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zm6 RCSB], [https://www.ebi.ac.uk/pdbsum/5zm6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/OSBL1_HUMAN OSBL1_HUMAN]] Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3-phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193).<ref>PMID:16176980</ref> <ref>PMID:17428193</ref>	+	[https://www.uniprot.org/uniprot/OSBL1_HUMAN OSBL1_HUMAN] Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3-phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193).<ref>PMID:16176980</ref> <ref>PMID:17428193</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Dong, J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Luo, Z~~]]	+	[[Category: Dong J]]
-	[[Category: ~~Wang, J~~]]	+	[[Category: Luo Z]]
-	[[Category: ~~Wu,~~ J W]]	+	[[Category: Wang J]]
-	[[Category: ~~Complex]]~~	+	[[Category: Wu JW]]
-	~~[[Category: Lipid transport]]~~	+
-	~~[[Category: Phospholipid]]~~	+
-	~~[[Category: Transporter~~]]	+

OCA at 08:17, 6 March 2019

OCA — Wed, 06 Mar 2019 08:17:51 GMT

←Older revision		Revision as of 08:17, 6 March 2019
Line 1:		Line 1:

	==Crystal structure of ORP1-ORD in complex with PI(4,5)P2==		==Crystal structure of ORP1-ORD in complex with PI(4,5)P2==
-	<StructureSection load='5zm6' size='340' side='right' caption='[[5zm6]], [[Resolution\|resolution]] 2.70Å' scene=''>	+	<StructureSection load='5zm6' size='340' side='right' caption='[[5zm6]], [[Resolution\|resolution]] 2.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zm6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zm6]] 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=5ZM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM6 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IEP:[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl]+icosa-5,8,11,14-tetraenoate'>IEP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IEP:[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl]+icosa-5,8,11,14-tetraenoate'>IEP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">OSBPL1A, ORP1, OSBP8, OSBPL1, OSBPL1B ([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=5zm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm6 OCA], [http://pdbe.org/5zm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm6 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm6 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=5zm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm6 OCA], [http://pdbe.org/5zm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm6 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/OSBL1_HUMAN OSBL1_HUMAN]] Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3-phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193).<ref>PMID:16176980</ref> <ref>PMID:17428193</ref>		[[http://www.uniprot.org/uniprot/OSBL1_HUMAN OSBL1_HUMAN]] Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3-phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193).<ref>PMID:16176980</ref> <ref>PMID:17428193</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phosphatidylinositol phosphates (PIPs) and cholesterol are known to regulate the function of late endosomes and lysosomes (LELs), and ORP1L specifically localizes to LELs. Here, we show in vitro that ORP1 is a PI(4,5)P2- or PI(3,4)P2-dependent cholesterol transporter, but cannot transport any PIPs. In cells, both ORP1L and PI(3,4)P2 are required for the efficient removal of cholesterol from LELs. Structures of the lipid-binding domain of ORP1 (ORP1-ORD) in complex with cholesterol or PI(4,5)P2 display open conformations essential for ORP function. PI(4,5)P2/PI(3,4)P2 can facilitate ORP1-mediated cholesterol transport by promoting membrane targeting and cholesterol extraction. Thus, our work unveils a distinct mechanism by which PIPs may allosterically enhance OSBP/ORPs-mediated transport of major lipid species such as cholesterol.
		+
		+	Allosteric enhancement of ORP1-mediated cholesterol transport by PI(4,5)P2/PI(3,4)P2.,Dong J, Du X, Wang H, Wang J, Lu C, Chen X, Zhu Z, Luo Z, Yu L, Brown AJ, Yang H, Wu JW Nat Commun. 2019 Feb 19;10(1):829. doi: 10.1038/s41467-019-08791-0. PMID:30783101<ref>PMID:30783101</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zm6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Dong, J]]		[[Category: Dong, J]]
	[[Category: Luo, Z]]		[[Category: Luo, Z]]

OCA at 15:12, 27 February 2019

OCA — Wed, 27 Feb 2019 15:12:42 GMT

←Older revision		Revision as of 15:12, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zm6 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of ORP1-ORD in complex with PI(4,5)P2==
-		+	<StructureSection load='5zm6' size='340' side='right' caption='[[5zm6]], [[Resolution\|resolution]] 2.70Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zm6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZM6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZM6 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=IEP:[(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl]+icosa-5,8,11,14-tetraenoate'>IEP</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=5zm6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zm6 OCA], [http://pdbe.org/5zm6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zm6 RCSB], [http://www.ebi.ac.uk/pdbsum/5zm6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zm6 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/OSBL1_HUMAN OSBL1_HUMAN]] Binds phospholipids; exhibits strong binding to phosphatidic acid and weak binding to phosphatidylinositol 3-phosphate (By similarity). Stabilizes GTP-bound RAB7A on late endosomes/lysosomes and alters functional properties of late endocytic compartments via its interaction with RAB7A (PubMed:16176980). Binds 25-hydroxycholesterol and cholesterol (PubMed:17428193).<ref>PMID:16176980</ref> <ref>PMID:17428193</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Dong, J]]
		+	[[Category: Luo, Z]]
		+	[[Category: Wang, J]]
		+	[[Category: Wu, J W]]
		+	[[Category: Complex]]
		+	[[Category: Lipid transport]]
		+	[[Category: Phospholipid]]
		+	[[Category: Transporter]]

OCA at 05:29, 29 August 2018

OCA — Wed, 29 Aug 2018 05:29:06 GMT

←Older revision		Revision as of 05:29, 29 August 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zm6 is ON HOLD	+	The entry 5zm6 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5zm6" [edit=sysop:move=sysop]

OCA — Wed, 11 Apr 2018 12:20:27 GMT

Protected "5zm6" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:20, 11 April 2018

OCA: New page: '''Unreleased structure''' The entry 5zm6 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 11 Apr 2018 12:20:26 GMT

New page: '''Unreleased structure''' The entry 5zm6 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5zm6 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]