7vgv - Revision history

OCA at 10:07, 6 September 2023

2023-09-06T10:07:23Z

←Older revision		Revision as of 10:07, 6 September 2023
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	<StructureSection load='7vgv' size='340' side='right'caption='[[7vgv]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='7vgv' size='340' side='right'caption='[[7vgv]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7vgv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vgv]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Nonlabens_marinus_S1-08 Nonlabens marinus S1-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</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'>[https://proteopedia.org/fgij/fg.htm?mol=7vgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgv OCA], [https://pdbe.org/7vgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgv RCSB], [https://www.ebi.ac.uk/pdbsum/7vgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgv 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=7vgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgv OCA], [https://pdbe.org/7vgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgv RCSB], [https://www.ebi.ac.uk/pdbsum/7vgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/W8VZW3_9FLAO W8VZW3_9FLAO]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hosaka, T]]	+	[[Category: Nonlabens marinus S1-08]]
-	[[Category: Kimura-Someya, T]]	+	[[Category: Hosaka T]]
-	[[Category: Luo, F]]	+	[[Category: Kimura-Someya T]]
-	[[Category: Nakane, T]]	+	[[Category: Luo F]]
-	[[Category: Nango, E]]	+	[[Category: Nakane T]]
-	[[Category: Shirouzu, M]]	+	[[Category: Nango E]]
-	~~[[Category: Membrane protein]]~~	+	[[Category: Shirouzu M]]
-	~~[[Category: Sacla serial femtosecond crystallography cell-free synthesis bacterial type rhodopsin chloride ion pump rhodopsin~~]]	+

OCA at 07:27, 9 March 2022

2022-03-09T07:27:57Z

←Older revision		Revision as of 07:27, 9 March 2022
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	==Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA==		==Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA==
-	<StructureSection load='7vgv' size='340' side='right'caption='[[7vgv]]' scene=''>	+	<StructureSection load='7vgv' size='340' side='right'caption='[[7vgv]], [[Resolution\|resolution]] 2.30Å' 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=7VGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7vgv]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGV FirstGlance]. <br>
-	</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=7vgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgv OCA], [https://pdbe.org/7vgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgv RCSB], [https://www.ebi.ac.uk/pdbsum/7vgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgv 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=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</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'>[https://proteopedia.org/fgij/fg.htm?mol=7vgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgv OCA], [https://pdbe.org/7vgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgv RCSB], [https://www.ebi.ac.uk/pdbsum/7vgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgv ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Light-driven chloride-pumping rhodopsins actively transport anions, including various halide ions, across cell membranes. Recent studies using time-resolved serial femtosecond crystallography (TR-SFX) have uncovered the structural changes and ion transfer mechanisms in light-driven cation-pumping rhodopsins. However, the mechanism by which the conformational changes pump an anion to achieve unidirectional ion transport, from the extracellular side to the cytoplasmic side, in anion-pumping rhodopsins remains enigmatic. We have collected TR-SFX data of Nonlabens marinus rhodopsin-3 (NM-R3), derived from a marine flavobacterium, at 10-micros and 1-ms time points after photoexcitation. Our structural analysis reveals the conformational alterations during ion transfer and after ion release. Movements of the retinal chromophore initially displace a conserved tryptophan to the cytoplasmic side of NM-R3, accompanied by a slight shift of the halide ion bound to the retinal. After ion release, the inward movements of helix C and helix G and the lateral displacements of the retinal block access to the extracellular side of NM-R3. Anomalous signal data have also been obtained from NM-R3 crystals containing iodide ions. The anomalous density maps provide insight into the halide binding site for ion transfer in NM-R3.
		+
		+	Conformational alterations in unidirectional ion transport of a light-driven chloride pump revealed using X-ray free electron lasers.,Hosaka T, Nomura T, Kubo M, Nakane T, Fangjia L, Sekine SI, Ito T, Murayama K, Ihara K, Ehara H, Kashiwagi K, Katsura K, Akasaka R, Hisano T, Tanaka T, Tanaka R, Arima T, Yamashita A, Sugahara M, Naitow H, Matsuura Y, Yoshizawa S, Tono K, Owada S, Nureki O, Kimura-Someya T, Iwata S, Nango E, Shirouzu M Proc Natl Acad Sci U S A. 2022 Mar 1;119(9). pii: 2117433119. doi:, 10.1073/pnas.2117433119. PMID:35197289<ref>PMID:35197289</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7vgv" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hosaka T]]	+	[[Category: Hosaka, T]]
-	[[Category: Kimura-Someya T]]	+	[[Category: Kimura-Someya, T]]
-	[[Category: Luo F]]	+	[[Category: Luo, F]]
-	[[Category: Nakane T]]	+	[[Category: Nakane, T]]
-	[[Category: Nango E]]	+	[[Category: Nango, E]]
-	[[Category: Shirouzu M]]	+	[[Category: Shirouzu, M]]
		+	[[Category: Membrane protein]]
		+	[[Category: Sacla serial femtosecond crystallography cell-free synthesis bacterial type rhodopsin chloride ion pump rhodopsin]]

OCA at 10:19, 16 February 2022

2022-02-16T10:19:34Z

←Older revision		Revision as of 10:19, 16 February 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7vgv is ~~ON HOLD until Paper Publication~~	+	==Anion free form of light-driven chloride ion-pumping rhodopsin, NM-R3, structure determined by serial femtosecond crystallography at SACLA==
-		+	<StructureSection load='7vgv' size='340' side='right'caption='[[7vgv]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VGV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VGV FirstGlance]. <br>
-	~~Description~~:	+	</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=7vgv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vgv OCA], [https://pdbe.org/7vgv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vgv RCSB], [https://www.ebi.ac.uk/pdbsum/7vgv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vgv ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Hosaka T]]
		+	[[Category: Kimura-Someya T]]
		+	[[Category: Luo F]]
		+	[[Category: Nakane T]]
		+	[[Category: Nango E]]
		+	[[Category: Shirouzu M]]

OCA at 04:21, 6 October 2021

2021-10-06T04:21:13Z

←Older revision		Revision as of 04:21, 6 October 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7vgv is ON HOLD	+	The entry 7vgv is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7vgv" [edit=sysop:move=sysop]

2021-09-29T07:52:59Z

Protected "7vgv" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:52, 29 September 2021

OCA: New page: '''Unreleased structure''' The entry 7vgv is ON HOLD Authors: Description: Category: Unreleased Structures

2021-09-29T07:52:58Z

New page: '''Unreleased structure''' The entry 7vgv is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7vgv is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]