5yk6 - Revision history

OCA at 10:23, 27 March 2024

OCA — Wed, 27 Mar 2024 10:23:48 GMT

←Older revision		Revision as of 10:23, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5yk6' size='340' side='right'caption='[[5yk6]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5yk6' size='340' side='right'caption='[[5yk6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yk6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5YK6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yk6]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zygosaccharomyces_rouxii_CBS_732 Zygosaccharomyces rouxii CBS 732]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YK6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</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]] 2.8Å</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=5yk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk6 OCA], [~~http~~://pdbe.org/5yk6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yk6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yk6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk6 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene></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=5yk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk6 OCA], [https://pdbe.org/5yk6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yk6 RCSB], [https://www.ebi.ac.uk/pdbsum/5yk6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MMM1_ZYGRC MMM1_ZYGRC]] Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis and may function in phospholipid exchange. The MDM12-MMM1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The MDM10-MDM12-MMM1 subcomplex further acts in the TOM40-specific pathway after the action of the MDM12-MMM1 complex. Essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids.	+	[https://www.uniprot.org/uniprot/MMM1_ZYGRC MMM1_ZYGRC] Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis and may function in phospholipid exchange. The MDM12-MMM1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The MDM10-MDM12-MMM1 subcomplex further acts in the TOM40-specific pathway after the action of the MDM12-MMM1 complex. Essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mmm1 and the Mdm12-Mmm1 complex at 2.8 A and 3.8 A resolution, respectively. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12-Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-A-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12-Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro.	+
-		+
-	Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites.,Jeong H, Park J, Jun Y, Lee C Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9502-E9511. doi:, 10.1073/pnas.1715592114. Epub 2017 Oct 25. PMID:29078410<ref>PMID:29078410</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yk6" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jeong, H~~]]	+	[[Category: Zygosaccharomyces rouxii CBS 732]]
-	[[Category: ~~Lee, C~~]]	+	[[Category: Jeong H]]
-	[[Category: ~~Park, J~~]]	+	[[Category: Lee C]]
-	[[Category: ~~Erme]]~~	+	[[Category: Park J]]
-	~~[[Category: Lipid transport]]~~	+
-	~~[[Category: Membrane contact site]]~~	+
-	~~[[Category: Phospholipid~~]]	+

OCA at 09:21, 21 October 2020

OCA — Wed, 21 Oct 2020 09:21:15 GMT

←Older revision		Revision as of 09:21, 21 October 2020
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	==Crystal Structure of Mmm1==		==Crystal Structure of Mmm1==
-	<StructureSection load='5yk6' size='340' side='right' caption='[[5yk6]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5yk6' size='340' side='right'caption='[[5yk6]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yk6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YK6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yk6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5YK6 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</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=5yk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk6 OCA], [http://pdbe.org/5yk6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk6 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=5yk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk6 OCA], [http://pdbe.org/5yk6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Jeong, H]]		[[Category: Jeong, H]]
	[[Category: Lee, C]]		[[Category: Lee, C]]

OCA at 08:29, 10 January 2018

OCA — Wed, 10 Jan 2018 08:29:47 GMT

←Older revision		Revision as of 08:29, 10 January 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yk6 is ~~ON HOLD until Paper~~ Publication	+	==Crystal Structure of Mmm1==
		+	<StructureSection load='5yk6' size='340' side='right' caption='[[5yk6]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5yk6]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YK6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YK6 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3PH:1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE'>3PH</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=5yk6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yk6 OCA], [http://pdbe.org/5yk6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yk6 RCSB], [http://www.ebi.ac.uk/pdbsum/5yk6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yk6 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MMM1_ZYGRC MMM1_ZYGRC]] Component of the ERMES/MDM complex, which serves as a molecular tether to connect the endoplasmic reticulum and mitochondria. Components of this complex are involved in the control of mitochondrial shape and protein biogenesis and may function in phospholipid exchange. The MDM12-MMM1 subcomplex functions in the major beta-barrel assembly pathway that is responsible for biogenesis of all outer membrane beta-barrel proteins, and acts in a late step after the SAM complex. The MDM10-MDM12-MMM1 subcomplex further acts in the TOM40-specific pathway after the action of the MDM12-MMM1 complex. Essential for establishing and maintaining the structure of mitochondria and maintenance of mtDNA nucleoids.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The endoplasmic reticulum (ER)-mitochondria encounter structure (ERMES) comprises mitochondrial distribution and morphology 12 (Mdm12), maintenance of mitochondrial morphology 1 (Mmm1), Mdm34, and Mdm10 and mediates physical membrane contact sites and nonvesicular lipid trafficking between the ER and mitochondria in yeast. Herein, we report two crystal structures of the synaptotagmin-like mitochondrial lipid-binding protein (SMP) domain of Mmm1 and the Mdm12-Mmm1 complex at 2.8 A and 3.8 A resolution, respectively. Mmm1 adopts a dimeric SMP structure augmented with two extra structural elements at the N and C termini that are involved in tight self-association and phospholipid coordination. Mmm1 binds two phospholipids inside the hydrophobic cavity, and the phosphate ion of the distal phospholipid is specifically recognized through extensive H-bonds. A positively charged concave surface on the SMP domain not only mediates ER membrane docking but also results in preferential binding to glycerophospholipids such as phosphatidylcholine (PC), phosphatidic acid (PA), phosphatidylglycerol (PG), and phosphatidylserine (PS), some of which are substrates for lipid-modifying enzymes in mitochondria. The Mdm12-Mmm1 structure reveals two Mdm12s binding to the SMP domains of the Mmm1 dimer in a pairwise head-to-tail manner. Direct association of Mmm1 and Mdm12 generates a 210-A-long continuous hydrophobic tunnel that facilitates phospholipid transport. The Mdm12-Mmm1 complex binds all glycerophospholipids except for phosphatidylethanolamine (PE) in vitro.

-	~~Authors: Jeong~~, H., Park, J., ~~Lee~~, C.	+	Crystal structures of Mmm1 and Mdm12-Mmm1 reveal mechanistic insight into phospholipid trafficking at ER-mitochondria contact sites.,Jeong H, Park J, Jun Y, Lee C Proc Natl Acad Sci U S A. 2017 Nov 7;114(45):E9502-E9511. doi:, 10.1073/pnas.1715592114. Epub 2017 Oct 25. PMID:29078410<ref>PMID:29078410</ref>

-	~~Description: Crystal Structure~~ of ~~Mmm1~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5yk6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jeong, H]]
	[[Category: Lee, C]]		[[Category: Lee, C]]
	[[Category: Park, J]]		[[Category: Park, J]]
-	[[Category: ~~Jeong, H~~]]	+	[[Category: Erme]]
		+	[[Category: Lipid transport]]
		+	[[Category: Membrane contact site]]
		+	[[Category: Phospholipid]]

OCA: Protected "5yk6" [edit=sysop:move=sysop]

OCA — Wed, 01 Nov 2017 04:43:30 GMT

Protected "5yk6" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:43, 1 November 2017

OCA: New page: '''Unreleased structure''' The entry 5yk6 is ON HOLD until Paper Publication Authors: Jeong, H., Park, J., Lee, C. Description: Crystal Structure of Mmm1 [[Category: Unreleased Structu...

OCA — Wed, 01 Nov 2017 04:43:29 GMT

New page: '''Unreleased structure''' The entry 5yk6 is ON HOLD until Paper Publication Authors: Jeong, H., Park, J., Lee, C. Description: Crystal Structure of Mmm1 [[Category: Unreleased Structu...

New page

'''Unreleased structure'''

The entry 5yk6 is ON HOLD until Paper Publication

Authors: Jeong, H., Park, J., Lee, C.

Description: Crystal Structure of Mmm1
[[Category: Unreleased Structures]]
[[Category: Lee, C]]
[[Category: Park, J]]
[[Category: Jeong, H]]