4y0l - Revision history

OCA at 13:02, 1 March 2024

2024-03-01T13:02:23Z

←Older revision		Revision as of 13:02, 1 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>		<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 2.4Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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'>[https://proteopedia.org/fgij/fg.htm?mol=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [https://pdbe.org/4y0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [https://www.ebi.ac.uk/pdbsum/4y0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0l 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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [https://pdbe.org/4y0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [https://www.ebi.ac.uk/pdbsum/4y0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>		[https://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II contains three soluble domains (D1, D2, and D3) and has two full-length members, MmpL3 and MmpL11. Significantly, MmpL3 is currently the most druggable M. tuberculosis target. We have solved the 2.4-A MmpL11-D2 crystal structure, revealing structural homology to periplasmic porter subdomains of RND (multidrug) transporters. The resulting predicted cluster II MmpL membrane topology has D1 and D2 residing, and possibly interacting, within the periplasm. Crosslinking and biolayer interferometry experiments confirm that cluster II D1 and D2 bind with weak affinities, and guided D1-D2 heterodimeric model assemblies. The predicted full-length MmpL3 and MmpL11 structural models reveal key substrate binding and transport residues, and may serve as templates to set the stage for in silico anti-tuberculosis drug development.
-
-	The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis.,Chim N, Torres R, Liu Y, Capri J, Batot G, Whitelegge JP, Goulding CW Chem Biol. 2015 Aug 20;22(8):1098-107. doi: 10.1016/j.chembiol.2015.07.013. Epub , 2015 Aug 13. PMID:26278184<ref>PMID:26278184</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4y0l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:01, 26 April 2023

2023-04-26T18:01:17Z

←Older revision		Revision as of 18:01, 26 April 2023
Line 3:		Line 3:
	<StructureSection load='4y0l' size='340' side='right'caption='[[4y0l]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4y0l' size='340' side='right'caption='[[4y0l]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mmpL11, Rv0202c, MTV033.10c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [https://pdbe.org/4y0l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [https://www.ebi.ac.uk/pdbsum/4y0l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0l 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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [~~http~~://pdbe.org/4y0l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4y0l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0l ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU]] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>	+	[https://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Chim, N]]	+	[[Category: Chim N]]
-	[[Category: Goulding~~, C W~~]]	+	[[Category: Goulding CW]]
-	[[Category: Torres, R]]	+	[[Category: Torres R]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Rnd family~~]]	+

OCA at 00:18, 6 June 2019

2019-06-06T00:18:09Z

←Older revision		Revision as of 00:18, 6 June 2019
Line 1:		Line 1:
		+
	==Mycobacterial membrane protein MmpL11D2==		==Mycobacterial membrane protein MmpL11D2==
-	<StructureSection load='4y0l' size='340' side='right' caption='[[4y0l]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4y0l' size='340' side='right'caption='[[4y0l]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [http://www.ebi.ac.uk/pdbsum/4y0l PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">mmpL11, Rv0202c, MTV033.10c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [http://pdbe.org/4y0l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [http://www.ebi.ac.uk/pdbsum/4y0l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4y0l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 18:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4y0l" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Chim, N]]		[[Category: Chim, N]]
	[[Category: Goulding, C W]]		[[Category: Goulding, C W]]

OCA at 06:34, 2 September 2015

2015-09-02T06:34:00Z

←Older revision		Revision as of 06:34, 2 September 2015
Line 8:		Line 8:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU]] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>		[[http://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU]] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mycobacterium tuberculosis mycobacterial membrane protein large (MmpL) proteins are important in substrate transport across the inner membrane. Here, we show that MmpL proteins are classified into two phylogenetic clusters, where MmpL cluster II contains three soluble domains (D1, D2, and D3) and has two full-length members, MmpL3 and MmpL11. Significantly, MmpL3 is currently the most druggable M. tuberculosis target. We have solved the 2.4-A MmpL11-D2 crystal structure, revealing structural homology to periplasmic porter subdomains of RND (multidrug) transporters. The resulting predicted cluster II MmpL membrane topology has D1 and D2 residing, and possibly interacting, within the periplasm. Crosslinking and biolayer interferometry experiments confirm that cluster II D1 and D2 bind with weak affinities, and guided D1-D2 heterodimeric model assemblies. The predicted full-length MmpL3 and MmpL11 structural models reveal key substrate binding and transport residues, and may serve as templates to set the stage for in silico anti-tuberculosis drug development.
		+
		+	The Structure and Interactions of Periplasmic Domains of Crucial MmpL Membrane Proteins from Mycobacterium tuberculosis.,Chim N, Torres R, Liu Y, Capri J, Batot G, Whitelegge JP, Goulding CW Chem Biol. 2015 Aug 20;22(8):1098-107. doi: 10.1016/j.chembiol.2015.07.013. Epub , 2015 Aug 13. PMID:26278184<ref>PMID:26278184</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 14:49, 12 August 2015

2015-08-12T14:49:59Z

←Older revision		Revision as of 14:49, 12 August 2015
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Mycobacterial membrane protein MmpL11D2==
-		+	<StructureSection load='4y0l' size='340' side='right' caption='[[4y0l]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~The entry~~ 4y0l is ~~ON HOLD until Paper Publication~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4y0l]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4Y0L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4Y0L FirstGlance]. <br>
-	~~Authors~~: ~~Torres~~, R., ~~Chim, N~~., ~~Goulding, C~~.W.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</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=4y0l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4y0l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4y0l RCSB], [http://www.ebi.ac.uk/pdbsum/4y0l PDBsum]</span></td></tr>
-	~~Description:~~	+	</table>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/MMPLB_MYCTU MMPLB_MYCTU]] Part of a heme-iron acquisition system. Receives heme from the heme-binding protein Rv0203 and transports it into the mycobacterial cell. Contributes to virulence.<ref>PMID:15908378</ref> <ref>PMID:21383189</ref> <ref>PMID:23760277</ref> Could also transport the mycolic acid-containing lipids monomeromycolyl diacylglycerol (MMDAG) and mycolate ester wax (WE) to the bacterial surface.<ref>PMID:23836904</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Chim, N]]		[[Category: Chim, N]]
-	[[Category: Goulding, C.W]]	+	[[Category: Goulding, C W]]
	[[Category: Torres, R]]		[[Category: Torres, R]]
		+	[[Category: Membrane protein]]
		+	[[Category: Rnd family]]

OCA at 09:00, 30 April 2015

2015-04-30T09:00:01Z

←Older revision		Revision as of 09:00, 30 April 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4y0l is ON HOLD	+	The entry 4y0l is ON HOLD until Paper Publication

	Authors: Torres, R., Chim, N., Goulding, C.W.		Authors: Torres, R., Chim, N., Goulding, C.W.

OCA at 09:58, 4 March 2015

2015-03-04T09:58:45Z

←Older revision		Revision as of 09:58, 4 March 2015
Line 3:		Line 3:
	The entry 4y0l is ON HOLD		The entry 4y0l is ON HOLD

-	Authors: Torres, R, Chim, ~~Nicholas~~, Goulding, C.W.	+	Authors: Torres, R., Chim, N., Goulding, C.W.

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: ~~Torres, R,~~ Chim, ~~Nicholas,~~ Goulding, C.W]]	+	[[Category: Chim, N]]
		+	[[Category: Goulding, C.W]]
		+	[[Category: Torres, R]]

OCA: Protected "4y0l" [edit=sysop:move=sysop]

2015-02-12T10:58:05Z

Protected "4y0l" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:58, 12 February 2015

OCA: New page: '''Unreleased structure''' The entry 4y0l is ON HOLD Authors: Torres, R, Chim, Nicholas, Goulding, C.W. Description: Category: Unreleased Structures [[Category: Torres, R, Chim, N...

2015-02-12T10:58:03Z

New page: '''Unreleased structure''' The entry 4y0l is ON HOLD Authors: Torres, R, Chim, Nicholas, Goulding, C.W. Description: Category: Unreleased Structures [[Category: Torres, R, Chim, N...

New page

'''Unreleased structure'''

The entry 4y0l is ON HOLD

Authors: Torres, R, Chim, Nicholas, Goulding, C.W.

Description:
[[Category: Unreleased Structures]]
[[Category: Torres, R, Chim, Nicholas, Goulding, C.W]]