5ydz - Revision history

OCA at 10:23, 27 March 2024

2024-03-27T10:23:03Z

←Older revision		Revision as of 10:23, 27 March 2024
Line 3:		Line 3:
	<SX load='5ydz' size='340' side='right' viewer='molstar' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>		<SX load='5ydz' size='340' side='right' viewer='molstar' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>
-	</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=5ydz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydz OCA], [~~http~~://pdbe.org/5ydz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ydz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ydz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydz ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 5.8Å</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=5ydz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydz OCA], [https://pdbe.org/5ydz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ydz RCSB], [https://www.ebi.ac.uk/pdbsum/5ydz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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]	+	[https://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.	+
-		+
-	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>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5ydz" style="background-color:#fffaf0;"></div>~~	+
	== References ==		== References ==
	<references/>		<references/>
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	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Gao, N~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Yang, M~~]]	+	[[Category: Gao N]]
-	[[Category: ~~Combined regulation mechanism]]~~	+	[[Category: Yang M]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Mtrpml1]]~~	+
-	~~[[Category: Mucolipidosis type iv]]~~	+
-	~~[[Category: Structual comparison~~]]	+

OCA at 22:42, 10 April 2020

2020-04-10T22:42:32Z

←Older revision		Revision as of 22:42, 10 April 2020
Line 3:		Line 3:
	<SX load='5ydz' size='340' side='right' viewer='molstar' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>		<SX load='5ydz' size='340' side='right' viewer='molstar' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>
-	</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=5ydz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydz OCA], [http://pdbe.org/5ydz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydz RCSB], [http://www.ebi.ac.uk/pdbsum/5ydz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydz ProSAT]</span></td></tr>	+	</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=5ydz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydz OCA], [http://pdbe.org/5ydz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydz RCSB], [http://www.ebi.ac.uk/pdbsum/5ydz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydz ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:13, 6 March 2020

2020-03-06T20:13:34Z

←Older revision		Revision as of 20:13, 6 March 2020
Line 1:		Line 1:

	==structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1==		==structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1==
-	<~~StructureSection~~ load='5ydz' size='340' side='right' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>	+	<SX load='5ydz' size='340' side='right' viewer='molstar' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Gao, N]]		[[Category: Gao, N]]
	[[Category: Yang, M]]		[[Category: Yang, M]]

OCA at 08:31, 27 December 2017

2017-12-27T08:31:45Z

←Older revision		Revision as of 08:31, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ydz is ~~ON HOLD until Paper~~ Publication	+	==structure of endo-lysosomal TRPML1 channel inserting into amphipol: state 1==
		+	<StructureSection load='5ydz' size='340' side='right' caption='[[5ydz]], [[Resolution\|resolution]] 5.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ydz]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YDZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YDZ FirstGlance]. <br>
		+	</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=5ydz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ydz OCA], [http://pdbe.org/5ydz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ydz RCSB], [http://www.ebi.ac.uk/pdbsum/5ydz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ydz 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~~:	+	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~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ydz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Gao, N]]
		+	[[Category: Yang, M]]
		+	[[Category: Combined regulation mechanism]]
		+	[[Category: Membrane protein]]
		+	[[Category: Mtrpml1]]
		+	[[Category: Mucolipidosis type iv]]
		+	[[Category: Structual comparison]]

OCA at 04:54, 29 November 2017

2017-11-29T04:54:08Z

←Older revision		Revision as of 04:54, 29 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2017-09-27T16:27:19Z

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

←Older revision

Revision as of 16:27, 27 September 2017

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

2017-09-27T16:27:18Z

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

New page

'''Unreleased structure'''

The entry 5ydz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]