6idp - Revision history

OCA at 10:32, 27 March 2024

OCA — Wed, 27 Mar 2024 10:32:46 GMT

←Older revision		Revision as of 10:32, 27 March 2024
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	==Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight form==		==Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight form==
-	<StructureSection load='6idp' size='340' side='right' caption='[[6idp]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='6idp' size='340' side='right'caption='[[6idp]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6idp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IDP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6idp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_cholerae Vibrio cholerae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IDP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=OLC:(2R)~~-2~~,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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]] 2.205Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CGT79_05080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~666~~ "~~Bacillo virgola del Koch~~" ~~Trevisan 1884]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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=6idp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idp OCA], [~~http~~://pdbe.org/6idp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6idp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6idp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6idp 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=6idp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idp OCA], [https://pdbe.org/6idp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6idp RCSB], [https://www.ebi.ac.uk/pdbsum/6idp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6idp ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na(+) or H(+) gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate transport mechanism remains controversial. Here we report crystal structures of VcmN, a Vibrio cholerae MATE transporter driven by the H(+) gradient. High-resolution structures in two distinct conformations associated with different pHs revealed that the rearrangement of the hydrogen-bonding network around the conserved Asp35 induces the bending of transmembrane helix 1, as in the case of the H(+)-coupled Pyrococcus furiosus MATE transporter. We also determined the crystal structure of the D35N mutant, which captured a unique conformation of TM1 facilitated by an altered hydrogen-bonding network. Based on the present results, we propose a common step in the transport cycle shared among prokaryotic H(+)-coupled MATE transporters.
-
-	Structural Basis of H(+)-Dependent Conformational Change in a Bacterial MATE Transporter.,Kusakizako T, Claxton DP, Tanaka Y, Maturana AD, Kuroda T, Ishitani R, Mchaourab HS, Nureki O Structure. 2018 Oct 30. pii: S0969-2126(18)30365-4. doi:, 10.1016/j.str.2018.10.004. PMID:30449688<ref>PMID:30449688</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6idp" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillo virgola del koch trevisan 1884~~]]	+	[[Category: Large Structures]]
-	[[Category: Claxton~~, D P~~]]	+	[[Category: Vibrio cholerae]]
-	[[Category: Ishitani, R]]	+	[[Category: Claxton DP]]
-	[[Category: Kuroda, T]]	+	[[Category: Ishitani R]]
-	[[Category: Kusakizako, T]]	+	[[Category: Kuroda T]]
-	[[Category: Maturana~~, A D~~]]	+	[[Category: Kusakizako T]]
-	[[Category: Mchaourab~~, H S~~]]	+	[[Category: Maturana AD]]
-	[[Category: Nureki, O]]	+	[[Category: Mchaourab HS]]
-	[[Category: Tanaka, Y]]	+	[[Category: Nureki O]]
-	~~[[Category: Mate multidrug transporter]]~~	+	[[Category: Tanaka Y]]
-	~~[[Category: Transport protein~~]]	+

OCA at 08:46, 21 February 2019

OCA — Thu, 21 Feb 2019 08:46:49 GMT

←Older revision		Revision as of 08:46, 21 February 2019
Line 3:		Line 3:
	<StructureSection load='6idp' size='340' side='right' caption='[[6idp]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='6idp' size='340' side='right' caption='[[6idp]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6idp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6idp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillo_virgola_del_koch"_trevisan_1884 "bacillo virgola del koch" trevisan 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CGT79_05080 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=666 "Bacillo virgola del Koch" Trevisan 1884])</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=6idp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idp OCA], [http://pdbe.org/6idp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6idp RCSB], [http://www.ebi.ac.uk/pdbsum/6idp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6idp 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=6idp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idp OCA], [http://pdbe.org/6idp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6idp RCSB], [http://www.ebi.ac.uk/pdbsum/6idp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6idp ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillo virgola del koch trevisan 1884]]
	[[Category: Claxton, D P]]		[[Category: Claxton, D P]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 12:11, 16 January 2019

OCA — Wed, 16 Jan 2019 12:11:03 GMT

←Older revision		Revision as of 12:11, 16 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6idp is ~~ON HOLD~~	+	==Crystal structure of Vibrio cholerae MATE transporter VcmN in the straight form==
		+	<StructureSection load='6idp' size='340' side='right' caption='[[6idp]], [[Resolution\|resolution]] 2.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6idp]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IDP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IDP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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=6idp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6idp OCA], [http://pdbe.org/6idp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6idp RCSB], [http://www.ebi.ac.uk/pdbsum/6idp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6idp ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Multidrug and toxic compound extrusion (MATE) transporters efflux toxic compounds using a Na(+) or H(+) gradient across the membrane. Although the structures of MATE transporters have been reported, the cation-coupled substrate transport mechanism remains controversial. Here we report crystal structures of VcmN, a Vibrio cholerae MATE transporter driven by the H(+) gradient. High-resolution structures in two distinct conformations associated with different pHs revealed that the rearrangement of the hydrogen-bonding network around the conserved Asp35 induces the bending of transmembrane helix 1, as in the case of the H(+)-coupled Pyrococcus furiosus MATE transporter. We also determined the crystal structure of the D35N mutant, which captured a unique conformation of TM1 facilitated by an altered hydrogen-bonding network. Based on the present results, we propose a common step in the transport cycle shared among prokaryotic H(+)-coupled MATE transporters.

-	~~Authors~~:	+	Structural Basis of H(+)-Dependent Conformational Change in a Bacterial MATE Transporter.,Kusakizako T, Claxton DP, Tanaka Y, Maturana AD, Kuroda T, Ishitani R, Mchaourab HS, Nureki O Structure. 2018 Oct 30. pii: S0969-2126(18)30365-4. doi:, 10.1016/j.str.2018.10.004. PMID:30449688<ref>PMID:30449688</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6idp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Claxton, D P]]
		+	[[Category: Ishitani, R]]
		+	[[Category: Kuroda, T]]
		+	[[Category: Kusakizako, T]]
		+	[[Category: Maturana, A D]]
		+	[[Category: Mchaourab, H S]]
		+	[[Category: Nureki, O]]
		+	[[Category: Tanaka, Y]]
		+	[[Category: Mate multidrug transporter]]
		+	[[Category: Transport protein]]

OCA: Protected "6idp" [edit=sysop:move=sysop]

OCA — Wed, 19 Sep 2018 18:18:43 GMT

Protected "6idp" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:18, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6idp is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Sep 2018 18:18:42 GMT

New page: '''Unreleased structure''' The entry 6idp is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6idp is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]