5ye5 - Revision history

OCA at 22:43, 10 April 2020

OCA — Fri, 10 Apr 2020 22:43:02 GMT

←Older revision		Revision as of 22:43, 10 April 2020
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	<SX load='5ye5' size='340' side='right' viewer='molstar' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>		<SX load='5ye5' size='340' side='right' viewer='molstar' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure with sequence from [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=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure with sequence from [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=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mcoln1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mcoln1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5ye5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ye5 OCA], [http://pdbe.org/5ye5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ye5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ye5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ye5 ProSAT]</span></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=5ye5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ye5 OCA], [http://pdbe.org/5ye5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ye5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ye5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ye5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:13, 6 March 2020

OCA — Fri, 06 Mar 2020 20:13:47 GMT

←Older revision		Revision as of 20:13, 6 March 2020
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	==structure of endo-lysosomal TRPML1 channel inserting into nanodisc==		==structure of endo-lysosomal TRPML1 channel inserting into nanodisc==
-	<~~StructureSection~~ load='5ye5' size='340' side='right' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>	+	<SX load='5ye5' size='340' side='right' viewer='molstar' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure with sequence from [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=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure with sequence from [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=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Gao, N]]		[[Category: Gao, N]]

OCA at 10:34, 22 November 2017

OCA — Wed, 22 Nov 2017 10:34:02 GMT

←Older revision		Revision as of 10:34, 22 November 2017
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	<StructureSection load='5ye5' size='340' side='right' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>		<StructureSection load='5ye5' size='340' side='right' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure with sequence from [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=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Mcoln1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=5ye5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ye5 OCA], [http://pdbe.org/5ye5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ye5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ye5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ye5 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=5ye5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ye5 OCA], [http://pdbe.org/5ye5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ye5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ye5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ye5 ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Gao, N]]		[[Category: Gao, N]]
	[[Category: Yang, M]]		[[Category: Yang, M]]

OCA at 07:39, 15 November 2017

OCA — Wed, 15 Nov 2017 07:39:11 GMT

←Older revision		Revision as of 07:39, 15 November 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5ye5 is ~~ON HOLD until Paper~~ Publication	+	==structure of endo-lysosomal TRPML1 channel inserting into nanodisc==
		+	<StructureSection load='5ye5' size='340' side='right' caption='[[5ye5]], [[Resolution\|resolution]] 5.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ye5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YE5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YE5 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=5ye5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ye5 OCA], [http://pdbe.org/5ye5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ye5 RCSB], [http://www.ebi.ac.uk/pdbsum/5ye5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ye5 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MCLN1_MOUSE MCLN1_MOUSE]] Nonselective cation channel probably playing a role in the regulation of membrane trafficking events and of metal homeostasis. Proposed to play a major role in Ca(2+) release from late endosome and lysosome vesicles to the cytoplasm, which is important for many lysosome-dependent cellular events, including the fusion and trafficking of these organelles, exocytosis and autophagy. Required for efficient uptake of large particles in macrophages in which Ca(2+) release from the lysosomes triggers lysosomal exocytosis. May also play a role in phagosome-lysosome fusion (PubMed:23993788). Involved in lactosylceramide trafficking indicative for a role in the regulation of late endocytic membrane fusion/fission events. By mediating lysosomal Ca(2+) release is involved in regulation of mTORC1 signaling and in mTOR/TFEB-dependent lysosomal adaptation to environmental cues such as nutrient levels (PubMed:25733853). Seems to act as lysosomal active oxygen species (ROS) sensor involved in ROS-induced TFEB activation and autophagy (By similarity). Functions as a Fe(2+) permeable channel in late endosomes and lysosomes. Proposed to play a role in zinc homeostasis probably implicating its association with TMEM163 (By similarity). In adaptive immunity, TRPML2 and TRPML1 may play redundant roles in the function of the specialized lysosomes of B cells (PubMed:17050035).[UniProtKB:Q9GZU1]<ref>PMID:17050035</ref> <ref>PMID:23993788</ref> <ref>PMID:25733853</ref> May contribute to cellular lipase activity within the late endosomal pathway or at the cell surface which may be involved in processes of membrane reshaping and vesiculation, especially the growth of tubular structures. However, it is not known, whether it conveys the enzymatic activity directly, or merely facilitates the activity of an associated phospholipase.[UniProtKB:Q9GZU1]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	TRPML1 channel is a non-selective group-2 transient receptor potential (TRP) channel with Ca2+ permeability. Located mainly in late endosome and lysosome of all mammalian cell types, TRPML1 is indispensable in the processes of endocytosis, membrane trafficking, and lysosome biogenesis. Mutations of TRPML1 cause a severe lysosomal storage disorder called mucolipidosis type IV (MLIV). In the present study, we determined the cryo-electron microscopy (cryo-EM) structures of Mus musculus TRPML1 (mTRPML1) in lipid nanodiscs and Amphipols. Two distinct states of mTRPML1 in Amphipols are added to the closed state, on which could represent two different confirmations upon activation and regulation. The polycystin-mucolipin domain (PMD) may sense the luminal/extracellular stimuli and undergo a "move upward" motion during endocytosis, thus triggering the overall conformational change in TRPML1. Based on the structural comparisons, we propose TRPML1 is regulated by pH, Ca2+, and phosphoinositides in a combined manner so as to accommodate the dynamic endocytosis process.

-	~~Authors: Yang, M~~., ~~Gao~~, N.	+	Cryo-EM structures of the mammalian endo-lysosomal TRPML1 channel elucidate the combined regulation mechanism.,Zhang S, Li N, Zeng W, Gao N, Yang M Protein Cell. 2017 Nov;8(11):834-847. doi: 10.1007/s13238-017-0476-5. Epub 2017, Sep 21. PMID:28936784<ref>PMID:28936784</ref>

-	~~Description: structure~~ of ~~endo-lysosomal TRPML1 channel inserting into nanodisc~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Yang, M]]~~	+	<div class="pdbe-citations 5ye5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gao, N]]		[[Category: Gao, N]]
		+	[[Category: Yang, M]]
		+	[[Category: Combined regulation mechanism]]
		+	[[Category: Membrane protein]]
		+	[[Category: Mtrpml1]]
		+	[[Category: Mucolipidosis type iv]]
		+	[[Category: Structual comparison]]

OCA at 06:24, 8 November 2017

OCA — Wed, 08 Nov 2017 06:24:20 GMT

←Older revision		Revision as of 06:24, 8 November 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ye5 is ON HOLD	+	The entry 5ye5 is ON HOLD until Paper Publication

	Authors: Yang, M., Gao, N.		Authors: Yang, M., Gao, N.

OCA at 05:34, 25 October 2017

OCA — Wed, 25 Oct 2017 05:34:18 GMT

←Older revision		Revision as of 05:34, 25 October 2017
Line 3:		Line 3:
	The entry 5ye5 is ON HOLD		The entry 5ye5 is ON HOLD

-	Authors: Yang, M., ~~Yang~~, ~~M., Yang, M~~.	+	Authors: Yang, M., Gao, N.

-	Description: structure of a lysosomal ~~protein~~	+	Description: structure of endo-lysosomal TRPML1 channel inserting into nanodisc
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Yang, M]]		[[Category: Yang, M]]
		+	[[Category: Gao, N]]

OCA: Protected "5ye5" [edit=sysop:move=sysop]

OCA — Wed, 27 Sep 2017 16:27:43 GMT

Protected "5ye5" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:27, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5ye5 is ON HOLD Authors: Yang, M., Yang, M., Yang, M. Description: structure of a lysosomal protein Category: Unreleased Structures [[Category:...

OCA — Wed, 27 Sep 2017 16:27:42 GMT

New page: '''Unreleased structure''' The entry 5ye5 is ON HOLD Authors: Yang, M., Yang, M., Yang, M. Description: structure of a lysosomal protein Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 5ye5 is ON HOLD

Authors: Yang, M., Yang, M., Yang, M.

Description: structure of a lysosomal protein
[[Category: Unreleased Structures]]
[[Category: Yang, M]]