5zih - Revision history

OCA at 08:56, 22 November 2023

OCA — Wed, 22 Nov 2023 08:56:48 GMT

←Older revision		Revision as of 08:56, 22 November 2023
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	==Crystal structure of the red light-activated channelrhodopsin Chrimson.==		==Crystal structure of the red light-activated channelrhodopsin Chrimson.==
-	<StructureSection load='5zih' size='340' side='right' caption='[[5zih]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5zih' size='340' side='right'caption='[[5zih]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zih]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Chlre Chlre~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZIH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zih]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlamydomonas_noctigama Chlamydomonas noctigama] and [https://en.wikipedia.org/wiki/Chlamydomonas_reinhardtii Chlamydomonas reinhardtii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZIH FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=OLC:(2R)~~-2~~,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</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]] 2.6Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">CSOA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3055 CHLRE])~~</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=5zih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zih OCA], [https://pdbe.org/5zih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zih RCSB], [https://www.ebi.ac.uk/pdbsum/5zih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zih 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=5zih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zih OCA], [~~http~~://pdbe.org/5zih PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zih RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zih PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zih ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q8L435_CHLRE Q8L435_CHLRE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chlre~~]]	+	[[Category: Chlamydomonas noctigama]]
-	[[Category: Hegemann, P]]	+	[[Category: Chlamydomonas reinhardtii]]
-	[[Category: Nishizawa, T]]	+	[[Category: Large Structures]]
-	[[Category: Nureki, O]]	+	[[Category: Hegemann P]]
-	[[Category: Oda, K]]	+	[[Category: Nishizawa T]]
-	[[Category: Oishi, S]]	+	[[Category: Nureki O]]
-	[[Category: Taniguchi, R]]	+	[[Category: Oda K]]
-	[[Category: Vierock, J]]	+	[[Category: Oishi S]]
-	[[Category: Yamashita, K]]	+	[[Category: Taniguchi R]]
-	~~[[Category: Ion channel]]~~	+	[[Category: Vierock J]]
-	~~[[Category: Membrane protein]]~~	+	[[Category: Yamashita K]]
-	~~[[Category: Rhodopsin~~]]	+

OCA at 20:50, 2 December 2018

OCA — Sun, 02 Dec 2018 20:50:36 GMT

←Older revision		Revision as of 20:50, 2 December 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zih is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the red light-activated channelrhodopsin Chrimson.==
		+	<StructureSection load='5zih' size='340' side='right' caption='[[5zih]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5zih]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlre Chlre]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZIH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZIH FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LYR:N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE'>LYR</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CSOA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3055 CHLRE])</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=5zih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zih OCA], [http://pdbe.org/5zih PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zih RCSB], [http://www.ebi.ac.uk/pdbsum/5zih PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zih ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Channelrhodopsins are light-activated ion channels that mediate cation permeation across cell membranes upon light absorption. Red-light-activated channelrhodopsins are of particular interest, because red light penetrates deeper into biological tissues and also enables dual-color experiments in combination with blue-light-activated optogenetic tools. Here we report the crystal structure of the most red-shifted channelrhodopsin from the algae Chlamydomonas noctigama, Chrimson, at 2.6 A resolution. Chrimson resembles prokaryotic proton pumps in the retinal binding pocket, while sharing similarity with other channelrhodopsins in the ion-conducting pore. Concomitant mutation analysis identified the structural features that are responsible for Chrimson's red light sensitivity; namely, the protonation of the counterion for the retinal Schiff base, and the polar residue distribution and rigidity of the retinal binding pocket. Based on these mechanistic insights, we engineered ChrimsonSA, a mutant with a maximum activation wavelength red-shifted beyond 605 nm and accelerated closing kinetics.

-	~~Authors~~:	+	Crystal structure of the red light-activated channelrhodopsin Chrimson.,Oda K, Vierock J, Oishi S, Rodriguez-Rozada S, Taniguchi R, Yamashita K, Wiegert JS, Nishizawa T, Hegemann P, Nureki O Nat Commun. 2018 Sep 26;9(1):3949. doi: 10.1038/s41467-018-06421-9. PMID:30258177<ref>PMID:30258177</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5zih" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Chlre]]
		+	[[Category: Hegemann, P]]
		+	[[Category: Nishizawa, T]]
		+	[[Category: Nureki, O]]
		+	[[Category: Oda, K]]
		+	[[Category: Oishi, S]]
		+	[[Category: Taniguchi, R]]
		+	[[Category: Vierock, J]]
		+	[[Category: Yamashita, K]]
		+	[[Category: Ion channel]]
		+	[[Category: Membrane protein]]
		+	[[Category: Rhodopsin]]

OCA at 12:17, 11 April 2018

OCA — Wed, 11 Apr 2018 12:17:49 GMT

←Older revision		Revision as of 12:17, 11 April 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 04:30, 4 April 2018

OCA — Wed, 04 Apr 2018 04:30:15 GMT

←Older revision		Revision as of 04:30, 4 April 2018
Line 3:		Line 3:
	The entry 5zih is ON HOLD		The entry 5zih is ON HOLD

-	Authors: ~~Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N., Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N.~~	+	Authors:

-	Description: ~~Crystal Structure of Protein~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Reiya, T]]
-	[[Category: Keitaro, Y]]
-	[[Category: Satomi, O]]
-	[[Category: Tomohiro, N]]
-	[[Category: Johannes, V]]
-	[[Category: Peter, H]]
-	[[Category: Kazumasa, O]]
-	[[Category: Osamu, N]]

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

OCA — Wed, 21 Mar 2018 06:03:19 GMT

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

←Older revision

Revision as of 06:03, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 5zih is ON HOLD Authors: Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N., Kazumasa, O., Johannes,...

OCA — Wed, 21 Mar 2018 06:03:18 GMT

New page: '''Unreleased structure''' The entry 5zih is ON HOLD Authors: Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N., Kazumasa, O., Johannes,...

New page

'''Unreleased structure'''

The entry 5zih is ON HOLD

Authors: Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N., Kazumasa, O., Johannes, V., Satomi, O., Reiya, T., Keitaro, Y., Tomohiro, N., Peter, H., Osamu, N.

Description: Crystal Structure of Protein
[[Category: Unreleased Structures]]
[[Category: Reiya, T]]
[[Category: Keitaro, Y]]
[[Category: Satomi, O]]
[[Category: Tomohiro, N]]
[[Category: Johannes, V]]
[[Category: Peter, H]]
[[Category: Kazumasa, O]]
[[Category: Osamu, N]]