6kkl - Revision history

OCA at 19:27, 29 May 2024

OCA — Wed, 29 May 2024 19:27:32 GMT

←Older revision		Revision as of 19:27, 29 May 2024
Line 3:		Line 3:
	<StructureSection load='6kkl' size='340' side='right'caption='[[6kkl]], [[Resolution\|resolution]] 2.65Å' scene=''>		<StructureSection load='6kkl' size='340' side='right'caption='[[6kkl]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[6kkl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli].~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KKL FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=BNG:B~~-~~NONYLGLUCOSIDE'>BNG</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]] 2.654Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~sotB, ydeA, b1528, JW1521 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=83333 ECOLI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</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=6kkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kkl OCA], [https://pdbe.org/6kkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kkl RCSB], [https://www.ebi.ac.uk/pdbsum/6kkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kkl 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=6kkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kkl OCA], [https://pdbe.org/6kkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kkl RCSB], [https://www.ebi.ac.uk/pdbsum/6kkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kkl ProSAT]</span></td></tr>
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/SOTB_ECOLI SOTB_ECOLI]] Involved in the efflux of sugars. The physiological role may be the reduction of the intracellular concentration of toxic sugars or sugar metabolites. Transports L-arabinose and to a lesser extent IPTG. Seems to contribute to the control of the arabinose regulon.
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Drug-proton antiporters (DHA) play an important role in multi-drug resistance, utilizing the proton-motive force to drive the expulsion of toxic molecules, including antibiotics and drugs. DHA transporters belong to the major facilitator superfamily (MFS), members of which deliver substrates by utilizing the alternating access model of transport. However, the transport process is still elusive. Here, we report the structures of SotB, a member of DHA1 family (TCDB: 2.A.1.2) from Escherichia coli. Four crystal structures of SotB were captured in different conformations, including substrate-bound occluded, inward-facing, and inward-open states. Comparisons between the four structures reveal nonlinear rigid-body movements of alternating access during the state transition from inward-open to occluded conformation. This work not only reveals the conformational dynamics of SotB but also deepens our understanding of the alternating access mechanism of MFS transporters.
-
-	Visualizing the nonlinear changes of a drug-proton antiporter from inward-open to occluded state.,Xiao Q, Sun B, Zhou Y, Wang C, Guo L, He J, Deng D Biochem Biophys Res Commun. 2021 Jan 1;534:272-278. doi:, 10.1016/j.bbrc.2020.11.096. Epub 2020 Dec 3. PMID:33280821<ref>PMID:33280821</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6kkl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deng, D]]	+	[[Category: Deng D]]
-	[[Category: Guo, L]]	+	[[Category: Guo L]]
-	[[Category: He~~, J H~~]]	+	[[Category: He JH]]
-	[[Category: Sun, B]]	+	[[Category: Sun B]]
-	[[Category: Xiao~~, Q J~~]]	+	[[Category: Xiao QJ]]
-	[[Category: Zuo~~, Y X]]~~	+	[[Category: Zuo YX]]
-	~~[[Category: Mfs antiporter]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 10:39, 31 March 2021

OCA — Wed, 31 Mar 2021 10:39:42 GMT

←Older revision		Revision as of 10:39, 31 March 2021
Line 1:		Line 1:

	==Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward conformation (H115N mutant)==		==Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward conformation (H115N mutant)==
-	<StructureSection load='6kkl' size='340' side='right'caption='[[6kkl]]' scene=''>	+	<StructureSection load='6kkl' size='340' side='right'caption='[[6kkl]], [[Resolution\|resolution]] 2.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6KKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6kkl]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KKL 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=6kkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kkl OCA], [~~http~~://pdbe.org/6kkl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kkl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kkl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kkl ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BNG:B-NONYLGLUCOSIDE'>BNG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">sotB, ydeA, b1528, JW1521 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=6kkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kkl OCA], [https://pdbe.org/6kkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kkl RCSB], [https://www.ebi.ac.uk/pdbsum/6kkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kkl ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/SOTB_ECOLI SOTB_ECOLI]] Involved in the efflux of sugars. The physiological role may be the reduction of the intracellular concentration of toxic sugars or sugar metabolites. Transports L-arabinose and to a lesser extent IPTG. Seems to contribute to the control of the arabinose regulon.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Drug-proton antiporters (DHA) play an important role in multi-drug resistance, utilizing the proton-motive force to drive the expulsion of toxic molecules, including antibiotics and drugs. DHA transporters belong to the major facilitator superfamily (MFS), members of which deliver substrates by utilizing the alternating access model of transport. However, the transport process is still elusive. Here, we report the structures of SotB, a member of DHA1 family (TCDB: 2.A.1.2) from Escherichia coli. Four crystal structures of SotB were captured in different conformations, including substrate-bound occluded, inward-facing, and inward-open states. Comparisons between the four structures reveal nonlinear rigid-body movements of alternating access during the state transition from inward-open to occluded conformation. This work not only reveals the conformational dynamics of SotB but also deepens our understanding of the alternating access mechanism of MFS transporters.
		+
		+	Visualizing the nonlinear changes of a drug-proton antiporter from inward-open to occluded state.,Xiao Q, Sun B, Zhou Y, Wang C, Guo L, He J, Deng D Biochem Biophys Res Commun. 2021 Jan 1;534:272-278. doi:, 10.1016/j.bbrc.2020.11.096. Epub 2020 Dec 3. PMID:33280821<ref>PMID:33280821</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kkl" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deng D]]	+	[[Category: Deng, D]]
-	[[Category: Guo L]]	+	[[Category: Guo, L]]
-	[[Category: He JH]]	+	[[Category: He, J H]]
-	[[Category: Sun B]]	+	[[Category: Sun, B]]
-	[[Category: Xiao QJ]]	+	[[Category: Xiao, Q J]]
-	[[Category: Zuo YX]]	+	[[Category: Zuo, Y X]]
		+	[[Category: Mfs antiporter]]
		+	[[Category: Transport protein]]

OCA at 11:06, 29 July 2020

OCA — Wed, 29 Jul 2020 11:06:23 GMT

←Older revision		Revision as of 11:06, 29 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6kkl is ON HOLD until Paper Publication~~	+	==Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward conformation (H115N mutant)==
-		+	<StructureSection load='6kkl' size='340' side='right'caption='[[6kkl]]' scene=''>
-	~~Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KKL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6KKL FirstGlance]. <br>
-	~~Description:~~ Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward conformation (H115N mutant)	+	</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=6kkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kkl OCA], [http://pdbe.org/6kkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kkl RCSB], [http://www.ebi.ac.uk/pdbsum/6kkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kkl ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Deng, D]]	+	__TOC__
-	[[Category: ~~He, J.H~~]]	+	</StructureSection>
-	[[Category: ~~Zuo, Y.X~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Guo, L~~]]	+	[[Category: Deng D]]
-	[[Category: Xiao~~, Q.J~~]]	+	[[Category: Guo L]]
-	[[Category: ~~Sun, B~~]]	+	[[Category: He JH]]
		+	[[Category: Sun B]]
		+	[[Category: Xiao QJ]]
		+	[[Category: Zuo YX]]

OCA at 05:45, 22 July 2020

OCA — Wed, 22 Jul 2020 05:45:59 GMT

←Older revision		Revision as of 05:45, 22 July 2020
Line 5:		Line 5:
	Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.		Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.

-	Description: ~~Structure~~ of ~~MFS transporter at 2.65 Angstroem resolution~~	+	Description: Crystal structure of Drug:Proton Antiporter-1 (DHA1) Family SotB, in the inward conformation (H115N mutant)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Deng, D]]		[[Category: Deng, D]]
		+	[[Category: He, J.H]]
		+	[[Category: Zuo, Y.X]]
	[[Category: Guo, L]]		[[Category: Guo, L]]
	[[Category: Xiao, Q.J]]		[[Category: Xiao, Q.J]]
	[[Category: Sun, B]]		[[Category: Sun, B]]
-	[[Category: He, J.H]]
-	[[Category: Zuo, Y.X]]

OCA at 07:16, 30 October 2019

OCA — Wed, 30 Oct 2019 07:16:35 GMT

←Older revision		Revision as of 07:16, 30 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kkl is ON HOLD	+	The entry 6kkl is ON HOLD until Paper Publication

	Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.		Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Deng, D]]		[[Category: Deng, D]]
-	[[Category: He, J.H]]
-	[[Category: Zuo, Y.X]]
	[[Category: Guo, L]]		[[Category: Guo, L]]
	[[Category: Xiao, Q.J]]		[[Category: Xiao, Q.J]]
	[[Category: Sun, B]]		[[Category: Sun, B]]
		+	[[Category: He, J.H]]
		+	[[Category: Zuo, Y.X]]

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

OCA — Wed, 31 Jul 2019 04:39:49 GMT

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

←Older revision

Revision as of 04:39, 31 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kkl is ON HOLD Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D. Description: Structure of MFS transporter at 2.65 Angstroem re...

OCA — Wed, 31 Jul 2019 04:39:48 GMT

New page: '''Unreleased structure''' The entry 6kkl is ON HOLD Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D. Description: Structure of MFS transporter at 2.65 Angstroem re...

New page

'''Unreleased structure'''

The entry 6kkl is ON HOLD

Authors: Xiao, Q.J., Sun, B., Zuo, Y.X., Guo, L., He, J.H., Deng, D.

Description: Structure of MFS transporter at 2.65 Angstroem resolution
[[Category: Unreleased Structures]]
[[Category: Deng, D]]
[[Category: He, J.H]]
[[Category: Zuo, Y.X]]
[[Category: Guo, L]]
[[Category: Xiao, Q.J]]
[[Category: Sun, B]]