6s63 - Revision history

OCA at 12:35, 24 January 2024

OCA — Wed, 24 Jan 2024 12:35:59 GMT

←Older revision		Revision as of 12:35, 24 January 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6s63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorubrum_sodomense Halorubrum sodomense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S63 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6s63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorubrum_sodomense Halorubrum sodomense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S63 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=~~R16~~:~~HEXADECANE~~'>~~R16~~</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]] 1.85Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~PCA~~:~~PYROGLUTAMIC+ACID~~'>~~PCA~~</scene~~></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6gux\|6gux]], [[6guz\|6guz]]</div~~></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=6s63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s63 OCA], [https://pdbe.org/6s63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s63 RCSB], [https://www.ebi.ac.uk/pdbsum/6s63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s63 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=6s63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s63 OCA], [https://pdbe.org/6s63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s63 RCSB], [https://www.ebi.ac.uk/pdbsum/6s63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s63 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/BACR3_HALSD BACR3_HALSD]] Light-driven proton pump.	+	[https://www.uniprot.org/uniprot/BACR3_HALSD BACR3_HALSD] Light-driven proton pump.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	[[Category: Halorubrum sodomense]]		[[Category: Halorubrum sodomense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Axford, D]]	+	[[Category: Axford D]]
-	[[Category: Juarez~~, J F.Bada~~]]	+	[[Category: Bada Juarez JF]]
-	[[Category: Judge~~, P J~~]]	+	[[Category: Judge PJ]]
-	[[Category: Moraes, I]]	+	[[Category: Moraes I]]
-	[[Category: Vinals, J]]	+	[[Category: Vinals J]]
-	[[Category: Watts, A]]	+	[[Category: Watts A]]
-	~~[[Category: Archaerhodopsin]]~~	+
-	~~[[Category: Lcp]]~~	+
-	~~[[Category: Membrane protein]]~~	+
-	~~[[Category: Proton transport]]~~	+
-	~~[[Category: Retinal]]~~	+
-	~~[[Category: Rhodopsin]]~~	+
-	~~[[Category: Room temperature]]~~	+
-	~~[[Category: Synchrotron~~]]	+

OCA at 07:33, 19 January 2022

OCA — Wed, 19 Jan 2022 07:33:48 GMT

←Older revision		Revision as of 07:33, 19 January 2022
Line 1:		Line 1:

	==Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature==		==Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature==
-	<StructureSection load='6s63' size='340' side='right'caption='[[6s63]]' scene=''>	+	<StructureSection load='6s63' size='340' side='right'caption='[[6s63]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S63 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6S63 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6s63]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halorubrum_sodomense Halorubrum sodomense]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S63 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6S63 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6s63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s63 OCA], [~~http~~://pdbe.org/6s63 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6s63 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6s63 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6s63 ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=R16:HEXADECANE'>R16</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6gux\|6gux]], [[6guz\|6guz]]</div></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=6s63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s63 OCA], [https://pdbe.org/6s63 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6s63 RCSB], [https://www.ebi.ac.uk/pdbsum/6s63 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6s63 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/BACR3_HALSD BACR3_HALSD]] Light-driven proton pump.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Room-temperature diffraction methods are highly desirable for dynamic studies of biological macromolecules, since they allow high-resolution structural data to be collected as proteins undergo conformational changes. For crystals grown in lipidic cubic phase (LCP), an extruder is commonly used to pass a stream of microcrystals through the X-ray beam; however, the sample quantities required for this method may be difficult to produce for many membrane proteins. A more sample-efficient environment was created using two layers of low X-ray transmittance polymer films to mount crystals of the archaerhodopsin-3 (AR3) photoreceptor and room-temperature diffraction data were acquired. By using transparent and opaque polymer films, two structures, one corresponding to the desensitized, dark-adapted (DA) state and the other to the ground or light-adapted (LA) state, were solved to better than 1.9 A resolution. All of the key structural features of AR3 were resolved, including the retinal chromophore, which is present as the 13-cis isomer in the DA state and as the all-trans isomer in the LA state. The film-sandwich sample environment enables diffraction data to be recorded at room temperature in both illuminated and dark conditions, which more closely approximate those in vivo. This simple approach is applicable to a wide range of membrane proteins crystallized in LCP and light-sensitive samples in general at synchrotron and laboratory X-ray sources.
		+
		+	Two states of a light-sensitive membrane protein captured at room temperature using thin-film sample mounts.,Axford D, Judge PJ, Bada Juarez JF, Kwan TOC, Birch J, Vinals J, Watts A, Moraes I Acta Crystallogr D Struct Biol. 2022 Jan 1;78(Pt 1):52-58. doi:, 10.1107/S2059798321011220. Epub 2022 Jan 1. PMID:34981761<ref>PMID:34981761</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6s63" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Bacteriorhodopsin 3D structures\|Bacteriorhodopsin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Halorubrum sodomense]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Axford D]]	+	[[Category: Axford, D]]
-	[[Category: ~~Bada~~ Juarez JF]]	+	[[Category: Juarez, J F.Bada]]
-	[[Category: Judge PJ]]	+	[[Category: Judge, P J]]
-	[[Category: Moraes I]]	+	[[Category: Moraes, I]]
-	[[Category: Vinals J]]	+	[[Category: Vinals, J]]
-	[[Category: Watts A]]	+	[[Category: Watts, A]]
		+	[[Category: Archaerhodopsin]]
		+	[[Category: Lcp]]
		+	[[Category: Membrane protein]]
		+	[[Category: Proton transport]]
		+	[[Category: Retinal]]
		+	[[Category: Rhodopsin]]
		+	[[Category: Room temperature]]
		+	[[Category: Synchrotron]]

OCA at 10:47, 22 July 2020

OCA — Wed, 22 Jul 2020 10:47:36 GMT

←Older revision		Revision as of 10:47, 22 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6s63 is ON HOLD until Paper Publication~~	+	==Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature==
-		+	<StructureSection load='6s63' size='340' side='right'caption='[[6s63]]' scene=''>
-	~~Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6S63 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6S63 FirstGlance]. <br>
-	~~Description:~~ Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6s63 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6s63 OCA], [http://pdbe.org/6s63 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6s63 RCSB], [http://www.ebi.ac.uk/pdbsum/6s63 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6s63 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Bada Juarez~~, J.F]]	+	__TOC__
-	[[Category: ~~Vinals, J~~]]	+	</StructureSection>
-	[[Category: ~~Watts, A~~]]	+	[[Category: Large Structures]]
-	[[Category: Judge~~, P.J~~]]	+	[[Category: Axford D]]
-	[[Category: Moraes, I]]	+	[[Category: Bada Juarez JF]]
-	[[Category: ~~Axford, D~~]]	+	[[Category: Judge PJ]]
		+	[[Category: Moraes I]]
		+	[[Category: Vinals J]]
		+	[[Category: Watts A]]

OCA at 09:14, 17 July 2019

OCA — Wed, 17 Jul 2019 09:14:37 GMT

←Older revision		Revision as of 09:14, 17 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6s63 is ON HOLD	+	The entry 6s63 is ON HOLD until Paper Publication

	Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A.		Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A.

OCA: Protected "6s63" [edit=sysop:move=sysop]

OCA — Wed, 10 Jul 2019 04:27:14 GMT

Protected "6s63" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:27, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6s63 is ON HOLD Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A. Description: Dark-adapted structure of Archa...

OCA — Wed, 10 Jul 2019 04:27:13 GMT

New page: '''Unreleased structure''' The entry 6s63 is ON HOLD Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A. Description: Dark-adapted structure of Archa...

New page

'''Unreleased structure'''

The entry 6s63 is ON HOLD

Authors: Moraes, I., Judge, P.J., Axford, D., Bada Juarez, J.F., Vinals, J., Watts, A.

Description: Dark-adapted structure of Archaerhodopsin-3 obtained from LCP crystals using a thin-film sandwich at room temperature
[[Category: Unreleased Structures]]
[[Category: Bada Juarez, J.F]]
[[Category: Vinals, J]]
[[Category: Watts, A]]
[[Category: Judge, P.J]]
[[Category: Moraes, I]]
[[Category: Axford, D]]