6tk5 - Revision history

OCA at 13:03, 24 January 2024

OCA — Wed, 24 Jan 2024 13:03:48 GMT

←Older revision		Revision as of 13:03, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6tk5' size='340' side='right'caption='[[6tk5]], [[Resolution\|resolution]] 2.25Å' scene=''>		<StructureSection load='6tk5' size='340' side='right'caption='[[6tk5]], [[Resolution\|resolution]] 2.25Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6tk5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Cip_108743 Cip 108743~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6TK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tk5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dokdonia_eikasta Dokdonia eikasta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6TK5 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=LFA:EICOSANE'>LFA</scene>~~, ~~<scene name='pdbligand=RET:RETINAL'>RET</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]] 2.25Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~NaR ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=308116 CIP 108743])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></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=6tk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk5 OCA], [~~http~~://pdbe.org/6tk5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6tk5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6tk5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk5 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=6tk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk5 OCA], [https://pdbe.org/6tk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6tk5 RCSB], [https://www.ebi.ac.uk/pdbsum/6tk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk5 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/N0DKS8_9FLAO N0DKS8_9FLAO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6tk5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6tk5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Cip 108743~~]]	+	[[Category: Dokdonia eikasta]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Benoit, R]]	+	[[Category: Benoit R]]
-	[[Category: Bruenle, S]]	+	[[Category: Bruenle S]]
-	[[Category: Cirelli, C]]	+	[[Category: Cirelli C]]
-	[[Category: Deupi, X]]	+	[[Category: Deupi X]]
-	[[Category: Dworkowski, F]]	+	[[Category: Dworkowski F]]
-	[[Category: Ehrenberg, D]]	+	[[Category: Ehrenberg D]]
-	[[Category: Furrer, A]]	+	[[Category: Furrer A]]
-	[[Category: Gashi, D]]	+	[[Category: Gashi D]]
-	[[Category: Gruhl, T]]	+	[[Category: Gruhl T]]
-	[[Category: Heberle, J]]	+	[[Category: Heberle J]]
-	[[Category: James, D]]	+	[[Category: James D]]
-	[[Category: Johnson, P]]	+	[[Category: Johnson P]]
-	[[Category: Kar, R]]	+	[[Category: Kar R]]
-	[[Category: Kekilli, D]]	+	[[Category: Kekilli D]]
-	[[Category: Knopp, G]]	+	[[Category: Knopp G]]
-	[[Category: Martiel, I]]	+	[[Category: Martiel I]]
-	[[Category: Milne, C]]	+	[[Category: Milne C]]
-	[[Category: Mous, S]]	+	[[Category: Mous S]]
-	[[Category: Nass, K]]	+	[[Category: Nass K]]
-	[[Category: Nogly, P]]	+	[[Category: Nogly P]]
-	[[Category: Ozerov, D]]	+	[[Category: Ozerov D]]
-	[[Category: Panneels, V]]	+	[[Category: Panneels V]]
-	[[Category: Schapiro, I]]	+	[[Category: Schapiro I]]
-	[[Category: Schertler~~, G F.X~~]]	+	[[Category: Schertler GFX]]
-	[[Category: Skopintsev, P]]	+	[[Category: Skopintsev P]]
-	[[Category: Standfuss, J]]	+	[[Category: Standfuss J]]
-	[[Category: Weinert, T]]	+	[[Category: Weinert T]]
-	[[Category: Wranik, M]]	+	[[Category: Wranik M]]
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Room-temperature]]~~	+
-	~~[[Category: Serial femtosecond crystallograpy]]~~	+
-	~~[[Category: Sodium pumping rhodopsin]]~~	+
-	~~[[Category: Time-resolved~~]]	+

OCA at 10:40, 17 June 2020

OCA — Wed, 17 Jun 2020 10:40:08 GMT

←Older revision		Revision as of 10:40, 17 June 2020
Line 1:		Line 1:

	==Femtosecond to millisecond structural changes in a light-driven sodium pump: 800fs+2ps structure of KR2 with extrapolated, light and dark datasets==		==Femtosecond to millisecond structural changes in a light-driven sodium pump: 800fs+2ps structure of KR2 with extrapolated, light and dark datasets==
-	<StructureSection load='6tk5' size='340' side='right'caption='[[6tk5]]' scene=''>	+	<StructureSection load='6tk5' size='340' side='right'caption='[[6tk5]], [[Resolution\|resolution]] 2.25Å' 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=6TK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TK5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6tk5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Cip_108743 Cip 108743]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TK5 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=6tk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk5 OCA], [http://pdbe.org/6tk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6tk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk5 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=LFA:EICOSANE'>LFA</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">NaR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=308116 CIP 108743])</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=6tk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk5 OCA], [http://pdbe.org/6tk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6tk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Light-driven sodium pumps actively transport small cations across cellular membranes(1). These pumps are used by microorganisms to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. Although the resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved(2,3), it is unclear how structural alterations over time allow sodium to be translocated against a concentration gradient. Here, using the Swiss X-ray Free Electron Laser(4), we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. High-resolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data, in combination with quantum chemical calculations, indicate that a sodium ion binds transiently close to the retinal within one millisecond. In the last structural intermediate, at 20 milliseconds after activation, we identified a potential second sodium-binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.
		+
		+	Femtosecond-to-millisecond structural changes in a light-driven sodium pump.,Skopintsev P, Ehrenberg D, Weinert T, James D, Kar RK, Johnson PJM, Ozerov D, Furrer A, Martiel I, Dworkowski F, Nass K, Knopp G, Cirelli C, Arrell C, Gashi D, Mous S, Wranik M, Gruhl T, Kekilli D, Brunle S, Deupi X, Schertler GFX, Benoit RM, Panneels V, Nogly P, Schapiro I, Milne C, Heberle J, Standfuss J Nature. 2020 May 20. pii: 10.1038/s41586-020-2307-8. doi:, 10.1038/s41586-020-2307-8. PMID:32499654<ref>PMID:32499654</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6tk5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Cip 108743]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Benoit R]]	+	[[Category: Benoit, R]]
-	[[Category: Bruenle S]]	+	[[Category: Bruenle, S]]
-	[[Category: Cirelli C]]	+	[[Category: Cirelli, C]]
-	[[Category: Deupi X]]	+	[[Category: Deupi, X]]
-	[[Category: Dworkowski F]]	+	[[Category: Dworkowski, F]]
-	[[Category: Ehrenberg D]]	+	[[Category: Ehrenberg, D]]
-	[[Category: Furrer A]]	+	[[Category: Furrer, A]]
-	[[Category: Gashi D]]	+	[[Category: Gashi, D]]
-	[[Category: Gruhl T]]	+	[[Category: Gruhl, T]]
-	[[Category: Heberle J]]	+	[[Category: Heberle, J]]
-	[[Category: James D]]	+	[[Category: James, D]]
-	[[Category: Johnson P]]	+	[[Category: Johnson, P]]
-	[[Category: Kar R]]	+	[[Category: Kar, R]]
-	[[Category: Kekilli D]]	+	[[Category: Kekilli, D]]
-	[[Category: Knopp G]]	+	[[Category: Knopp, G]]
-	[[Category: Martiel I]]	+	[[Category: Martiel, I]]
-	[[Category: Milne C]]	+	[[Category: Milne, C]]
-	[[Category: Mous S]]	+	[[Category: Mous, S]]
-	[[Category: Nass K]]	+	[[Category: Nass, K]]
-	[[Category: Nogly P]]	+	[[Category: Nogly, P]]
-	[[Category: Ozerov D]]	+	[[Category: Ozerov, D]]
-	[[Category: Panneels V]]	+	[[Category: Panneels, V]]
-	[[Category: Schapiro I]]	+	[[Category: Schapiro, I]]
-	[[Category: Schertler ~~GFX~~]]	+	[[Category: Schertler, G F.X]]
-	[[Category: Skopintsev P]]	+	[[Category: Skopintsev, P]]
-	[[Category: Standfuss J]]	+	[[Category: Standfuss, J]]
-	[[Category: Weinert T]]	+	[[Category: Weinert, T]]
-	[[Category: Wranik M]]	+	[[Category: Wranik, M]]
		+	[[Category: Membrane protein]]
		+	[[Category: Room-temperature]]
		+	[[Category: Serial femtosecond crystallograpy]]
		+	[[Category: Sodium pumping rhodopsin]]
		+	[[Category: Time-resolved]]

OCA at 06:58, 27 May 2020

OCA — Wed, 27 May 2020 06:58:49 GMT

←Older revision		Revision as of 06:58, 27 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6tk5 is ~~ON HOLD~~	+	==Femtosecond to millisecond structural changes in a light-driven sodium pump: 800fs+2ps structure of KR2 with extrapolated, light and dark datasets==
-		+	<StructureSection load='6tk5' size='340' side='right'caption='[[6tk5]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6TK5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6TK5 FirstGlance]. <br>
-	~~Description~~:	+	</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=6tk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6tk5 OCA], [http://pdbe.org/6tk5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6tk5 RCSB], [http://www.ebi.ac.uk/pdbsum/6tk5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6tk5 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Benoit R]]
		+	[[Category: Bruenle S]]
		+	[[Category: Cirelli C]]
		+	[[Category: Deupi X]]
		+	[[Category: Dworkowski F]]
		+	[[Category: Ehrenberg D]]
		+	[[Category: Furrer A]]
		+	[[Category: Gashi D]]
		+	[[Category: Gruhl T]]
		+	[[Category: Heberle J]]
		+	[[Category: James D]]
		+	[[Category: Johnson P]]
		+	[[Category: Kar R]]
		+	[[Category: Kekilli D]]
		+	[[Category: Knopp G]]
		+	[[Category: Martiel I]]
		+	[[Category: Milne C]]
		+	[[Category: Mous S]]
		+	[[Category: Nass K]]
		+	[[Category: Nogly P]]
		+	[[Category: Ozerov D]]
		+	[[Category: Panneels V]]
		+	[[Category: Schapiro I]]
		+	[[Category: Schertler GFX]]
		+	[[Category: Skopintsev P]]
		+	[[Category: Standfuss J]]
		+	[[Category: Weinert T]]
		+	[[Category: Wranik M]]

OCA: Protected "6tk5" [edit=sysop:move=sysop]

OCA — Wed, 04 Dec 2019 06:28:56 GMT

Protected "6tk5" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:28, 4 December 2019

OCA: New page: '''Unreleased structure''' The entry 6tk5 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 04 Dec 2019 06:28:54 GMT

New page: '''Unreleased structure''' The entry 6tk5 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6tk5 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]