OCA at 07:16, 22 March 2023

2023-03-22T07:16:38Z

←Older revision		Revision as of 07:16, 22 March 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 7xjd is ~~ON HOLD~~	+	==Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation==
		+	<StructureSection load='7xjd' size='340' side='right'caption='[[7xjd]], [[Resolution\|resolution]] 1.33Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[7xjd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum_NRC-1 Halobacterium salinarum NRC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7XJD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7XJD FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=SQU:2,10,23-TRIMETHYL-TETRACOSANE'>SQU</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=7xjd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7xjd OCA], [https://pdbe.org/7xjd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7xjd RCSB], [https://www.ebi.ac.uk/pdbsum/7xjd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7xjd ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The K intermediate of proton pumping bacteriorhodopsin is the first intermediate generated after isomerization of retinal to the 13-cis form. Although various structures have been reported for the K intermediate until now, these differ from each other, especially in terms of the conformation of the retinal chromophore and its interaction with surrounding residues. We report here an accurate X-ray crystallographic analysis of the K structure. The polyene chain of 13-cis retinal is observed to be S-shaped. The side chain of Lys216, which is covalently bound to retinal via the Schiff-base linkage, interacts with residues, Asp85 and Thr89. In addition, the Nzeta-H of the protonated Schiff-base linkage interacts with a residue, Asp212 and a water molecule, W402. Based on quantum chemical calculations for this K structure, we examine the stabilizing factors of distorted conformation of retinal and propose a relaxation manner to the next L intermediate.

-	~~Authors: Taguchi~~, S., Niwa, S., Takeda, K.	+	Detailed analysis of distorted retinal and its interaction with surrounding residues in the K intermediate of bacteriorhodopsin.,Taguchi S, Niwa S, Dao HA, Tanaka Y, Takeda R, Fukai S, Hasegawa K, Takeda K Commun Biol. 2023 Feb 17;6(1):190. doi: 10.1038/s42003-023-04554-2. PMID:36808185<ref>PMID:36808185</ref>

-	~~Description: Crystal structure~~ of ~~bacteriorhodopsin in~~ the ~~ground state by red laser irradiation~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Takeda, K~~]]	+	<div class="pdbe-citations 7xjd" style="background-color:#fffaf0;"></div>
-	[[Category: Taguchi, S]]	+	== References ==
-	[[Category: ~~Niwa, S~~]]	+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Halobacterium salinarum NRC-1]]
		+	[[Category: Large Structures]]
		+	[[Category: Niwa S]]
		+	[[Category: Taguchi S]]
		+	[[Category: Takeda K]]

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

2022-04-27T10:32:50Z

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

←Older revision

Revision as of 10:32, 27 April 2022

OCA: New page: '''Unreleased structure''' The entry 7xjd is ON HOLD Authors: Taguchi, S., Niwa, S., Takeda, K. Description: Crystal structure of bacteriorhodopsin in the ground state by red laser irr...

2022-04-27T10:32:49Z

New page: '''Unreleased structure''' The entry 7xjd is ON HOLD Authors: Taguchi, S., Niwa, S., Takeda, K. Description: Crystal structure of bacteriorhodopsin in the ground state by red laser irr...

New page

'''Unreleased structure'''

The entry 7xjd is ON HOLD

Authors: Taguchi, S., Niwa, S., Takeda, K.

Description: Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation
[[Category: Unreleased Structures]]
[[Category: Takeda, K]]
[[Category: Taguchi, S]]
[[Category: Niwa, S]]

7xjd - Revision history

OCA at 07:16, 22 March 2023

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

OCA: New page: '''Unreleased structure''' The entry 7xjd is ON HOLD Authors: Taguchi, S., Niwa, S., Takeda, K. Description: Crystal structure of bacteriorhodopsin in the ground state by red laser irr...