5b2n - Revision history

OCA at 15:57, 8 November 2023

OCA — Wed, 08 Nov 2023 15:57:24 GMT

←Older revision		Revision as of 15:57, 8 November 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5b2n]] is a 1 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=5B2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B2N FirstGlance]. <br>		<table><tr><td colspan='2'>[[5b2n]] is a 1 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=5B2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B2N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</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]] 1.581Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [https://pdbe.org/5b2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [https://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n 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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [https://pdbe.org/5b2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [https://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n ProSAT]</span></td></tr>
	</table>		</table>

OCA at 06:36, 31 May 2023

OCA — Wed, 31 May 2023 06:36:43 GMT

←Older revision		Revision as of 06:36, 31 May 2023
Line 3:		Line 3:
	<StructureSection load='5b2n' size='340' side='right'caption='[[5b2n]], [[Resolution\|resolution]] 1.58Å' scene=''>		<StructureSection load='5b2n' size='340' side='right'caption='[[5b2n]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b2n]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Flavobacteria_bacterium_s1~~-08 ~~Flavobacteria bacterium s1~~-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B2N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5B2N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b2n]] is a 1 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=5B2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5B2N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ClR, NMS_1267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1454201 Flavobacteria bacterium S1-08])</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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [https://pdbe.org/5b2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [https://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n 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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [~~http~~://pdbe.org/5b2n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n 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 ==
Line 24:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Flavobacteria bacterium s1-08]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Hosaka, T~~]]	+	[[Category: Nonlabens marinus S1-08]]
-	[[Category: ~~Kimura-Someya,~~ T]]	+	[[Category: Hosaka T]]
-	[[Category: ~~Shirouzu, M]]~~	+	[[Category: Kimura-Someya T]]
-	~~[[Category: Cell~~-~~free synthesis~~]]	+	[[Category: Shirouzu M]]
-	[[Category: ~~Light-driven chloride pump]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 10:01, 26 February 2020

OCA — Wed, 26 Feb 2020 10:01:58 GMT

←Older revision		Revision as of 10:01, 26 February 2020
Line 1:		Line 1:

	==Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus==		==Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus==
-	<StructureSection load='5b2n' size='340' side='right' caption='[[5b2n]], [[Resolution\|resolution]] 1.58Å' scene=''>	+	<StructureSection load='5b2n' size='340' side='right'caption='[[5b2n]], [[Resolution\|resolution]] 1.58Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5b2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B2N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5b2n]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavobacteria_bacterium_s1-08 Flavobacteria bacterium s1-08]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B2N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ClR, NMS_1267 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1454201 Flavobacteria bacterium S1-08])</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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [http://pdbe.org/5b2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [http://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n 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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [http://pdbe.org/5b2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [http://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n ProSAT]</span></td></tr>
	</table>		</table>
Line 16:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 5b2n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5b2n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Rhodopsin 3D structures\|Rhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Flavobacteria bacterium s1-08]]
		+	[[Category: Large Structures]]
	[[Category: Hosaka, T]]		[[Category: Hosaka, T]]
	[[Category: Kimura-Someya, T]]		[[Category: Kimura-Someya, T]]

OCA at 04:58, 9 September 2016

OCA — Fri, 09 Sep 2016 04:58:58 GMT

←Older revision		Revision as of 04:58, 9 September 2016
Line 7:		Line 7:
	<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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [http://pdbe.org/5b2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [http://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n 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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [http://pdbe.org/5b2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [http://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The light-driven inward chloride ion-pumping rhodopsin Nonlabens marinus rhodopsin-3 (NM-R3), from a marine flavobacterium, belongs to a phylogenetic lineage distinct from the halorhodopsins known as archaeal inward chloride ion-pumping rhodopsins. NM-R3 and halorhodopsin have distinct motif sequences that are important for chloride ion binding and transport. In this study, we present the crystal structure of a new type of light-driven chloride ion pump, NM-R3, at 1.58 A resolution. The structure revealed the chloride ion translocation pathway and showed that a single chloride ion resides near the Schiff base. The overall structure, chloride ion-binding site, and translocation pathway of NM-R3 are different from those of halorhodopsin. Unexpectedly, this NM-R3 structure is similar to the crystal structure of the light-driven outward sodium ion pump, Krokinobacter eikastus rhodopsin 2. Structural and mutational analyses of NM-R3 revealed that most of the important amino acid residues for chloride ion pumping exist in the ion influx region, located on the extracellular side of NM-R3. In contrast, on the opposite side, the cytoplasmic regions of K. eikastus rhodopsin 2 were reportedly important for sodium ion pumping. These results provide new insight into ion selection mechanisms in ion pumping rhodopsins, in which the ion influx regions of both the inward and outward pumps are important for their ion selectivities.
		+
		+	Structural Mechanism for Light-driven Transport by a New Type of Chloride Ion Pump, Nonlabens marinus Rhodopsin-3.,Hosaka T, Yoshizawa S, Nakajima Y, Ohsawa N, Hato M, DeLong EF, Kogure K, Yokoyama S, Kimura-Someya T, Iwasaki W, Shirouzu M J Biol Chem. 2016 Aug 19;291(34):17488-95. doi: 10.1074/jbc.M116.728220. Epub, 2016 Jun 30. PMID:27365396<ref>PMID:27365396</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5b2n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 11:40, 14 July 2016

OCA — Thu, 14 Jul 2016 11:40:57 GMT

←Older revision		Revision as of 11:40, 14 July 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5b2n is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of the light-driven chloride ion-pumping rhodopsin, ClP, from Nonlabens marinus==
-		+	<StructureSection load='5b2n' size='340' side='right' caption='[[5b2n]], [[Resolution\|resolution]] 1.58Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5b2n]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5B2N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5B2N FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=D12:DODECANE'>D12</scene>, <scene name='pdbligand=HEX:HEXANE'>HEX</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5b2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5b2n OCA], [http://pdbe.org/5b2n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5b2n RCSB], [http://www.ebi.ac.uk/pdbsum/5b2n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5b2n ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Hosaka, T]]
		+	[[Category: Kimura-Someya, T]]
		+	[[Category: Shirouzu, M]]
		+	[[Category: Cell-free synthesis]]
		+	[[Category: Light-driven chloride pump]]
		+	[[Category: Membrane protein]]
		+	[[Category: Retinal]]
		+	[[Category: Transport protein]]

OCA at 11:05, 15 May 2016

OCA — Sun, 15 May 2016 11:05:09 GMT

←Older revision		Revision as of 11:05, 15 May 2016
Line 3:		Line 3:
	The entry 5b2n is ON HOLD until Paper Publication		The entry 5b2n is ON HOLD until Paper Publication

-	Authors: ~~Hosaka, T., Kimura-Someya, T., Shirouzu, M.~~	+	Authors:

	Description:		Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Kimura-Someya, T]]
-	[[Category: Shirouzu, M]]
-	[[Category: Hosaka, T]]

OCA at 10:08, 3 February 2016

OCA — Wed, 03 Feb 2016 10:08:56 GMT

←Older revision		Revision as of 10:08, 3 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5b2n is ON HOLD	+	The entry 5b2n is ON HOLD until Paper Publication

	Authors: Hosaka, T., Kimura-Someya, T., Shirouzu, M.		Authors: Hosaka, T., Kimura-Someya, T., Shirouzu, M.

OCA: Protected "5b2n" [edit=sysop:move=sysop]

OCA — Wed, 27 Jan 2016 21:04:24 GMT

Protected "5b2n" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:04, 27 January 2016

OCA: New page: '''Unreleased structure''' The entry 5b2n is ON HOLD Authors: Hosaka, T., Kimura-Someya, T., Shirouzu, M. Description: Category: Unreleased Structures [[Category: Kimura-Someya, T...

OCA — Wed, 27 Jan 2016 21:04:22 GMT

New page: '''Unreleased structure''' The entry 5b2n is ON HOLD Authors: Hosaka, T., Kimura-Someya, T., Shirouzu, M. Description: Category: Unreleased Structures [[Category: Kimura-Someya, T...

New page

'''Unreleased structure'''

The entry 5b2n is ON HOLD

Authors: Hosaka, T., Kimura-Someya, T., Shirouzu, M.

Description:
[[Category: Unreleased Structures]]
[[Category: Kimura-Someya, T]]
[[Category: Shirouzu, M]]
[[Category: Hosaka, T]]