6rak - Revision history

OCA at 05:26, 11 April 2020

2020-04-11T05:26:29Z

←Older revision		Revision as of 05:26, 11 April 2020
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	<SX load='6rak' size='340' side='right' viewer='molstar' caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>		<SX load='6rak' size='340' side='right' viewer='molstar' caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Alpaca Alpaca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6RAK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Alpaca Alpaca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6RAK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOV:ADP+ORTHOVANADATE'>AOV</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AOV:ADP+ORTHOVANADATE'>AOV</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0976 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), TT_C0977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0976 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), TT_C0977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=6rak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rak OCA], [http://pdbe.org/6rak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rak RCSB], [http://www.ebi.ac.uk/pdbsum/6rak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rak 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=6rak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rak OCA], [http://pdbe.org/6rak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rak RCSB], [http://www.ebi.ac.uk/pdbsum/6rak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rak ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:08, 7 March 2020

2020-03-07T00:08:31Z

←Older revision		Revision as of 00:08, 7 March 2020
Line 1:		Line 1:

	==Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing occluded conformation==		==Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing occluded conformation==
-	<~~StructureSection~~ load='6rak' size='340' side='right'caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>	+	<SX load='6rak' size='340' side='right' viewer='molstar' caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Alpaca Alpaca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAK FirstGlance]. <br>		<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Alpaca Alpaca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAK FirstGlance]. <br>
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	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]		[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
	[[Category: Alpaca]]		[[Category: Alpaca]]

OCA at 06:26, 7 August 2019

2019-08-07T06:26:15Z

←Older revision		Revision as of 06:26, 7 August 2019
Line 3:		Line 3:
	<StructureSection load='6rak' size='340' side='right'caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>		<StructureSection load='6rak' size='340' side='right'caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Alpaca Alpaca]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOV:ADP+ORTHOVANADATE'>AOV</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOV:ADP+ORTHOVANADATE'>AOV</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TT_C0976 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971]), TT_C0977 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=6rak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rak OCA], [http://pdbe.org/6rak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rak RCSB], [http://www.ebi.ac.uk/pdbsum/6rak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rak 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=6rak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rak OCA], [http://pdbe.org/6rak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rak RCSB], [http://www.ebi.ac.uk/pdbsum/6rak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rak ProSAT]</span></td></tr>
	</table>		</table>
Line 20:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
		+	[[Category: Alpaca]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Hofmann, S]]		[[Category: Hofmann, S]]

OCA at 06:32, 31 July 2019

2019-07-31T06:32:16Z

←Older revision		Revision as of 06:32, 31 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6rak is ~~ON HOLD~~	+	==Heterodimeric ABC exporter TmrAB in vanadate trapped outward-facing occluded conformation==
		+	<StructureSection load='6rak' size='340' side='right'caption='[[6rak]], [[Resolution\|resolution]] 3.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6rak]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RAK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RAK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AOV:ADP+ORTHOVANADATE'>AOV</scene>, <scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=6rak FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rak OCA], [http://pdbe.org/6rak PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rak RCSB], [http://www.ebi.ac.uk/pdbsum/6rak PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rak ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cryo-electron microscopy (cryo-EM) has the capacity to capture molecular machines in action(1-3). ATP-binding cassette (ABC) exporters are highly dynamic membrane proteins that extrude a wide range of substances from the cytosol(4-6) and thereby contribute to essential cellular processes, adaptive immunity and multidrug resistance(7,8). Despite their importance, the coupling of nucleotide binding, hydrolysis and release to the conformational dynamics of these proteins remains poorly resolved, especially for heterodimeric and/or asymmetric ABC exporters that are abundant in humans. Here we present eight high-resolution cryo-EM structures that delineate the full functional cycle of an asymmetric ABC exporter in a lipid environment. Cryo-EM analysis under active turnover conditions reveals distinct inward-facing (IF) conformations-one of them with a bound peptide substrate-and previously undescribed asymmetric post-hydrolysis states with dimerized nucleotide-binding domains and a closed extracellular gate. By decreasing the rate of ATP hydrolysis, we could capture an outward-facing (OF) open conformation-an otherwise transient state vulnerable to substrate re-entry. The ATP-bound pre-hydrolysis and vanadate-trapped states are conformationally equivalent; both comprise co-existing OF conformations with open and closed extracellular gates. By contrast, the post-hydrolysis states from the turnover experiment exhibit asymmetric ATP and ADP occlusion after phosphate release from the canonical site and display a progressive separation of the nucleotide-binding domains and unlocking of the intracellular gate. Our findings reveal that phosphate release, not ATP hydrolysis, triggers the return of the exporter to the IF conformation. By mapping the conformational landscape during active turnover, aided by mutational and chemical modulation of kinetic rates to trap the key intermediates, we resolved fundamental steps of the substrate translocation cycle of asymmetric ABC transporters.

-	~~Authors~~:	+	Conformation space of a heterodimeric ABC exporter under turnover conditions.,Hofmann S, Januliene D, Mehdipour AR, Thomas C, Stefan E, Bruchert S, Kuhn BT, Geertsma ER, Hummer G, Tampe R, Moeller A Nature. 2019 Jul;571(7766):580-583. doi: 10.1038/s41586-019-1391-0. Epub 2019 Jul, 17. PMID:31316210<ref>PMID:31316210</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6rak" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hofmann, S]]
		+	[[Category: Hummer, G]]
		+	[[Category: Januliene, D]]
		+	[[Category: Mehdipour, A R]]
		+	[[Category: Moeller, A]]
		+	[[Category: Tampe, R]]
		+	[[Category: Thomas, C]]
		+	[[Category: Atp-binding cassette transporter]]
		+	[[Category: Exporter]]
		+	[[Category: Heterodimer]]
		+	[[Category: Membrane protein]]
		+	[[Category: Transport protein]]

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

2019-04-17T04:22:20Z

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

←Older revision

Revision as of 04:22, 17 April 2019

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

2019-04-17T04:22:19Z

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

New page

'''Unreleased structure'''

The entry 6rak is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]