7xjd: Difference between revisions
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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... |
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The | ==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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.33Å</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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 7xjd" style="background-color:#fffaf0;"></div> | ||
[[Category: Taguchi | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Halobacterium salinarum NRC-1]] | |||
[[Category: Large Structures]] | |||
[[Category: Niwa S]] | |||
[[Category: Taguchi S]] | |||
[[Category: Takeda K]] | |||
Latest revision as of 06:55, 21 November 2024
Crystal structure of bacteriorhodopsin in the ground state by red laser irradiation
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