5vn9 - Revision history

OCA at 13:52, 4 October 2023

OCA — Wed, 04 Oct 2023 13:52:06 GMT

←Older revision		Revision as of 13:52, 4 October 2023
Line 1:		Line 1:

	==Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid==		==Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid==
-	<StructureSection load='5vn9' size='340' side='right' caption='[[5vn9]], [[Resolution\|resolution]] 2.59Å' scene=''>	+	<StructureSection load='5vn9' size='340' side='right'caption='[[5vn9]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vn9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Halsa Halsa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VN9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vn9]] is a 2 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=5VN9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VN9 FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.594Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vn7\|5vn7]]</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></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop, VNG_1467G ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=64091 HALSA])~~</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=5vn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn9 OCA], [https://pdbe.org/5vn9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vn9 RCSB], [https://www.ebi.ac.uk/pdbsum/5vn9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn9 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=5vn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn9 OCA], [~~http~~://pdbe.org/5vn9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vn9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vn9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn9 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.	+	[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5vn9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vn9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Halsa~~]]	+	[[Category: Halobacterium salinarum NRC-1]]
-	[[Category: Borshchevskiy, V]]	+	[[Category: Large Structures]]
-	[[Category: Cherezov, V]]	+	[[Category: Borshchevskiy V]]
-	[[Category: Ishchenko, A]]	+	[[Category: Cherezov V]]
-	[[Category: Kuklin, A]]	+	[[Category: Ishchenko A]]
-	[[Category: Lee~~, S C~~]]	+	[[Category: Kuklin A]]
-	[[Category: Mishin, A]]	+	[[Category: Lee SC]]
-	[[Category: Peng, L]]	+	[[Category: Mishin A]]
-	[[Category: Vlasov, A]]	+	[[Category: Peng L]]
-	[[Category: Zhang, Q]]	+	[[Category: Vlasov A]]
-	[[Category: Zinovev, E]]	+	[[Category: Zhang Q]]
-	~~[[Category: Membrane protein]]~~	+	[[Category: Zinovev E]]
-	~~[[Category: Retinal protein~~]]	+

OCA at 08:15, 17 January 2018

OCA — Wed, 17 Jan 2018 08:15:16 GMT

←Older revision		Revision as of 08:15, 17 January 2018
Line 3:		Line 3:
	<StructureSection load='5vn9' size='340' side='right' caption='[[5vn9]], [[Resolution\|resolution]] 2.59Å' scene=''>		<StructureSection load='5vn9' size='340' side='right' caption='[[5vn9]], [[Resolution\|resolution]] 2.59Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vn9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vn9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Halsa Halsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN9 FirstGlance]. <br>
	</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>		</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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vn7\|5vn7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vn7\|5vn7]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bop, VNG_1467G ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=64091 HALSA])</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=5vn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn9 OCA], [http://pdbe.org/5vn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn9 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=5vn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn9 OCA], [http://pdbe.org/5vn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.		[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lipidic cubic phase (LCP) has been widely recognized as a promising membrane-mimicking matrix for biophysical studies of membrane proteins and their crystallization in a lipidic environment. Application of this material to a wide variety of membrane proteins, however, is hindered due to a limited number of available host lipids, mostly monoacylglycerols (MAGs). Here, we designed, synthesized and characterized a series of chemically stable lipids resistant to hydrolysis, with properties complementary to the widely used MAGs. In order to assess their potential to serve as host lipids for crystallization, we characterized the phase properties and lattice parameters of mesophases made of two most promising lipids at a variety of different conditions by polarized light microscopy and small-angle X-ray scattering. Both lipids showed remarkable chemical stability and an extended LCP region in the phase diagram covering a wide range of temperatures down to 4 degrees C. One of these lipids has been used for crystallization and structure determination of a prototypical membrane protein bacteriorhodopsin at 4 degrees C and 20 degrees C.
		+
		+	Chemically Stable Lipids for Membrane Protein Crystallization.,Ishchenko A, Peng L, Zinovev E, Vlasov A, Lee SC, Kuklin A, Mishin A, Borshchevskiy V, Zhang Q, Cherezov V Cryst Growth Des. 2017 Jun 7;17(6):3502-3511. doi: 10.1021/acs.cgd.7b00458. Epub , 2017 May 12. PMID:29290736<ref>PMID:29290736</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vn9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halsa]]
	[[Category: Borshchevskiy, V]]		[[Category: Borshchevskiy, V]]
	[[Category: Cherezov, V]]		[[Category: Cherezov, V]]

OCA at 10:00, 10 September 2017

OCA — Sun, 10 Sep 2017 10:00:13 GMT

←Older revision		Revision as of 10:00, 10 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5vn9 is ON HOLD until Paper Publication~~	+	==Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid==
-		+	<StructureSection load='5vn9' size='340' side='right' caption='[[5vn9]], [[Resolution\|resolution]] 2.59Å' scene=''>
-	~~Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov, V.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vn9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VN9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VN9 FirstGlance]. <br>
-	~~Description:~~ Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid	+	</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>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5vn7\|5vn7]]</td></tr>
-	[[~~Category~~: ~~Kuklin~~, A]]	+	<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=5vn9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vn9 OCA], [http://pdbe.org/5vn9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vn9 RCSB], [http://www.ebi.ac.uk/pdbsum/5vn9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vn9 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Zinovev~~, E]]	+	</table>
-	[[~~Category~~: ~~Peng, L~~]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
		+	__TOC__
		+	</StructureSection>
	[[Category: Borshchevskiy, V]]		[[Category: Borshchevskiy, V]]
		+	[[Category: Cherezov, V]]
	[[Category: Ishchenko, A]]		[[Category: Ishchenko, A]]
		+	[[Category: Kuklin, A]]
		+	[[Category: Lee, S C]]
	[[Category: Mishin, A]]		[[Category: Mishin, A]]
-	[[Category: ~~Lee~~, ~~S.C~~]]	+	[[Category: Peng, L]]
-	[[Category: ~~Cherezov~~, V]]	+	[[Category: Vlasov, A]]
	[[Category: Zhang, Q]]		[[Category: Zhang, Q]]
-	[[Category: ~~Vlasov~~, A]]	+	[[Category: Zinovev, E]]
		+	[[Category: Membrane protein]]
		+	[[Category: Retinal protein]]

OCA at 11:39, 24 May 2017

OCA — Wed, 24 May 2017 11:39:22 GMT

←Older revision		Revision as of 11:39, 24 May 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vn9 is ON HOLD	+	The entry 5vn9 is ON HOLD until Paper Publication

	Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov, V.		Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov, V.

OCA: Protected "5vn9" [edit=sysop:move=sysop]

OCA — Wed, 10 May 2017 11:12:48 GMT

Protected "5vn9" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:12, 10 May 2017

OCA: New page: '''Unreleased structure''' The entry 5vn9 is ON HOLD Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov...

OCA — Wed, 10 May 2017 11:12:47 GMT

New page: '''Unreleased structure''' The entry 5vn9 is ON HOLD Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov...

New page

'''Unreleased structure'''

The entry 5vn9 is ON HOLD

Authors: Ishchenko, A., Peng, L., Zinovev, E., Vlasov, A., Lee, S.C., Kuklin, A., Mishin, A., Borshchevskiy, V., Zhang, Q., Cherezov, V.

Description: Structure of bacteriorhodopsin from crystals grown at 4 deg C using GlyNCOC15+4 as an LCP host lipid
[[Category: Unreleased Structures]]
[[Category: Kuklin, A]]
[[Category: Zinovev, E]]
[[Category: Peng, L]]
[[Category: Borshchevskiy, V]]
[[Category: Ishchenko, A]]
[[Category: Mishin, A]]
[[Category: Lee, S.C]]
[[Category: Cherezov, V]]
[[Category: Zhang, Q]]
[[Category: Vlasov, A]]