3vvp - Revision history

OCA at 12:39, 8 November 2023

OCA — Wed, 08 Nov 2023 12:39:38 GMT

←Older revision		Revision as of 12:39, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3vvp' size='340' side='right'caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='3vvp' size='340' side='right'caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BNU:6~~-~~BROMO-1-ETHYL-4-OXO-7-(PIPERAZIN-1-YL)-1~~,~~4-DIHYDROQUINOLINE-3-CARBOXYLIC+ACID'>BNU</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]] 2.91Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;'>[[3vvn\|3vvn]]~~, ~~[[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNU:6-BROMO-1-ETHYL-4-OXO-7-(PIPERAZIN-1-YL)-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC+ACID'>BNU</scene></td></tr>
-	~~<tr id='gene~~'>~~<td class="sblockLbl"><b>[[Gene\|Gene:]]~~</b>~~</td><td class="sblockDat">PF0708 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])~~</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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [https://pdbe.org/3vvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [https://www.ebi.ac.uk/pdbsum/3vvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvp 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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [https://pdbe.org/3vvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [https://www.ebi.ac.uk/pdbsum/3vvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvp ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8U2X0_PYRFU Q8U2X0_PYRFU]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Ishitani, R~~]]	+	[[Category: Pyrococcus furiosus]]
-	[[Category: ~~Nureki, O~~]]	+	[[Category: Ishitani R]]
-	[[Category: ~~Tanaka, Y~~]]	+	[[Category: Nureki O]]
-	[[Category: ~~Ligand-bound]]~~	+	[[Category: Tanaka Y]]
-	~~[[Category: Mate]]~~	+
-	~~[[Category: Multidrug transporter]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 19:06, 27 July 2022

OCA — Wed, 27 Jul 2022 19:06:39 GMT

←Older revision		Revision as of 19:06, 27 July 2022
Line 1:		Line 1:

	==Crystal structure of MATE in complex with Br-NRF==		==Crystal structure of MATE in complex with Br-NRF==
-	<StructureSection load='3vvp' size='340' side='right' caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>	+	<StructureSection load='3vvp' size='340' side='right'caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3vvp]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3VVP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3vvp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VVP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNU:6-BROMO-1-ETHYL-4-OXO-7-(PIPERAZIN-1-YL)-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC+ACID'>BNU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNU:6-BROMO-1-ETHYL-4-OXO-7-(PIPERAZIN-1-YL)-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC+ACID'>BNU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]], [[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3vvn\|3vvn]], [[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [~~http~~://pdbe.org/3vvp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3vvp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvp 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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [https://pdbe.org/3vvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [https://www.ebi.ac.uk/pdbsum/3vvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 23:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 43587]]		[[Category: Atcc 43587]]
		+	[[Category: Large Structures]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
	[[Category: Nureki, O]]		[[Category: Nureki, O]]

OCA at 15:59, 11 August 2016

OCA — Thu, 11 Aug 2016 15:59:26 GMT

←Older revision		Revision as of 15:59, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of MATE in complex with Br-NRF==		==Crystal structure of MATE in complex with Br-NRF==
	<StructureSection load='3vvp' size='340' side='right' caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='3vvp' size='340' side='right' caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]], [[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]], [[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [http://www.ebi.ac.uk/pdbsum/3vvp PDBsum]</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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [http://pdbe.org/3vvp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [http://www.ebi.ac.uk/pdbsum/3vvp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vvp ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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 3vvp" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:04, 20 January 2015

OCA — Tue, 20 Jan 2015 10:04:12 GMT

←Older revision		Revision as of 10:04, 20 January 2015
Line 1:		Line 1:
-	~~{{STRUCTURE_3vvp\| PDB=3vvp \| SCENE= }}~~	+	==Crystal structure of MATE in complex with Br-NRF==
-	===Crystal structure of MATE in complex with Br-NRF===	+	<StructureSection load='3vvp' size='340' side='right' caption='[[3vvp]], [[Resolution\|resolution]] 2.91Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23535598}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3vvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VVP FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BNU:6-BROMO-1-ETHYL-4-OXO-7-(PIPERAZIN-1-YL)-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC+ACID'>BNU</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3vvn\|3vvn]], [[3vvo\|3vvo]], [[3vvq\|3vvq]], [[3vvr\|3vvr]], [[3vvs\|3vvs]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF0708 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=3vvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vvp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3vvp RCSB], [http://www.ebi.ac.uk/pdbsum/3vvp PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical gradient of H(+) or Na(+) across the membrane. MATE transporters confer multidrug resistance to bacterial pathogens and cancer cells, thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine. Here we present the crystal structures of the H(+)-driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1-3.0 A resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.

-	~~==About this Structure==~~	+	Structural basis for the drug extrusion mechanism by a MATE multidrug transporter.,Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, Nureki O Nature. 2013 Apr 11;496(7444):247-51. doi: 10.1038/nature12014. Epub 2013 Mar 27. PMID:23535598<ref>PMID:23535598</ref>
-	~~[[3vvp]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Atcc_43587 Atcc 43587]~~. ~~Full crystallographic information is available from [http~~:/~~/oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3VVP OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023535598</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Atcc 43587]]		[[Category: Atcc 43587]]
-	[[Category: Ishitani, R.]]	+	[[Category: Ishitani, R]]
-	[[Category: Nureki, O.]]	+	[[Category: Nureki, O]]
-	[[Category: Tanaka, Y.]]	+	[[Category: Tanaka, Y]]
	[[Category: Ligand-bound]]		[[Category: Ligand-bound]]
	[[Category: Mate]]		[[Category: Mate]]
	[[Category: Multidrug transporter]]		[[Category: Multidrug transporter]]
	[[Category: Transport protein]]		[[Category: Transport protein]]

OCA at 06:15, 29 January 2014

OCA — Wed, 29 Jan 2014 06:15:35 GMT

←Older revision		Revision as of 06:15, 29 January 2014
Line 1:		Line 1:
	{{STRUCTURE_3vvp\| PDB=3vvp \| SCENE= }}		{{STRUCTURE_3vvp\| PDB=3vvp \| SCENE= }}
	===Crystal structure of MATE in complex with Br-NRF===		===Crystal structure of MATE in complex with Br-NRF===
		+	{{ABSTRACT_PUBMED_23535598}}

	==About this Structure==		==About this Structure==
-	[[3vvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bacteroides_caccae Bacteroides caccae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA].	+	[[3vvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA].
-	[[Category: ~~Bacteroides caccae~~]]	+
		+	==Reference==
		+	<ref group="xtra">PMID:023535598</ref><references group="xtra"/><references/>
		+	[[Category: Atcc 43587]]
	[[Category: Ishitani, R.]]		[[Category: Ishitani, R.]]
	[[Category: Nureki, O.]]		[[Category: Nureki, O.]]

OCA at 01:39, 4 April 2013

OCA — Thu, 04 Apr 2013 01:39:15 GMT

←Older revision		Revision as of 01:39, 4 April 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_3vvp\| PDB=3vvp \| SCENE= }}
		+	===Crystal structure of MATE in complex with Br-NRF===

-	~~The entry~~ 3vvp is ~~ON HOLD until Paper Publication~~	+	==About this Structure==
-		+	[[3vvp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteroides_caccae Bacteroides caccae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VVP OCA].
-	~~Authors~~: ~~Tanaka, Y.,~~ Ishitani, R., Nureki, O.	+	[[Category: Bacteroides caccae]]
-		+	[[Category: Ishitani, R.]]
-	~~Description~~: ~~Crystal structure of membrane~~ protein	+	[[Category: Nureki, O.]]
		+	[[Category: Tanaka, Y.]]
		+	[[Category: Ligand-bound]]
		+	[[Category: Mate]]
		+	[[Category: Multidrug transporter]]
		+	[[Category: Transport protein]]

OCA at 19:55, 26 September 2012

OCA — Wed, 26 Sep 2012 19:55:42 GMT

←Older revision		Revision as of 19:55, 26 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3vvp is ON HOLD	+	The entry 3vvp is ON HOLD until Paper Publication

	Authors: Tanaka, Y., Ishitani, R., Nureki, O.		Authors: Tanaka, Y., Ishitani, R., Nureki, O.

	Description: Crystal structure of membrane protein		Description: Crystal structure of membrane protein

OCA: Protected "3vvp" [edit=sysop:move=sysop]

OCA — Wed, 01 Aug 2012 05:15:30 GMT

Protected "3vvp" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:15, 1 August 2012

OCA: New page: '''Unreleased structure''' The entry 3vvp is ON HOLD Authors: Tanaka, Y., Ishitani, R., Nureki, O. Description: Crystal structure of membrane protein

OCA — Wed, 01 Aug 2012 05:15:29 GMT

New page: '''Unreleased structure''' The entry 3vvp is ON HOLD Authors: Tanaka, Y., Ishitani, R., Nureki, O. Description: Crystal structure of membrane protein

New page

'''Unreleased structure'''

The entry 3vvp is ON HOLD

Authors: Tanaka, Y., Ishitani, R., Nureki, O.

Description: Crystal structure of membrane protein