4ybu - Revision history

OCA at 07:56, 27 September 2023

OCA — Wed, 27 Sep 2023 07:56:26 GMT

←Older revision		Revision as of 07:56, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBU FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 1.924Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RET:RETINAL'>RET</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [https://pdbe.org/4ybu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [https://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu 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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [https://pdbe.org/4ybu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [https://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:07, 3 May 2023

OCA — Wed, 03 May 2023 08:07:53 GMT

←Older revision		Revision as of 08:07, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4ybu' size='340' side='right'caption='[[4ybu]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='4ybu' size='340' side='right'caption='[[4ybu]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YBU FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [https://pdbe.org/4ybu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [https://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRABP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [~~http~~://pdbe.org/4ybu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RABP2_HUMAN RABP2_HUMAN]] Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.	+	[https://www.uniprot.org/uniprot/RABP2_HUMAN RABP2_HUMAN] Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Geiger~~, J H~~]]	+	[[Category: Geiger JH]]
-	[[Category: Nosrati, M]]	+	[[Category: Nosrati M]]
-	~~[[Category: Photoswitchable protein]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Retinal iminium pka change by isomerization]]~~	+
-	~~[[Category: Retinal isomerization]]~~	+
-	~~[[Category: Retinal psb]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 07:03, 12 June 2019

OCA — Wed, 12 Jun 2019 07:03:37 GMT

←Older revision		Revision as of 07:03, 12 June 2019
Line 1:		Line 1:

	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom - 1st cycle==		==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom - 1st cycle==
-	<StructureSection load='4ybu' size='340' side='right' caption='[[4ybu]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='4ybu' size='340' side='right'caption='[[4ybu]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CRABP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [http://pdbe.org/4ybu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [http://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu 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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [http://pdbe.org/4ybu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [http://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4ybu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ybu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cellular retinoic acid-binding protein 3D structures\|Cellular retinoic acid-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Geiger, J H]]		[[Category: Geiger, J H]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]

OCA at 17:42, 12 July 2016

OCA — Tue, 12 Jul 2016 17:42:29 GMT

←Older revision		Revision as of 17:42, 12 July 2016
Line 6:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [http://pdbe.org/4ybu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [http://www.ebi.ac.uk/pdbsum/4ybu PDBsum]</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [http://pdbe.org/4ybu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [http://www.ebi.ac.uk/pdbsum/4ybu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ybu ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RABP2_HUMAN RABP2_HUMAN]] Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.		[[http://www.uniprot.org/uniprot/RABP2_HUMAN RABP2_HUMAN]] Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.
		+
		+	A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.,Nosrati M, Berbasova T, Vasileiou C, Borhan B, Geiger JH J Am Chem Soc. 2016 Jul 5. PMID:27310917<ref>PMID:27310917</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4ybu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:50, 9 March 2016

OCA — Wed, 09 Mar 2016 19:50:37 GMT

←Older revision		Revision as of 19:50, 9 March 2016
Line 12:		Line 12:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Geiger, J]]	+	[[Category: Geiger, J H]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]
	[[Category: Photoswitchable protein]]		[[Category: Photoswitchable protein]]

OCA at 18:15, 26 February 2016

OCA — Fri, 26 Feb 2016 18:15:14 GMT

←Older revision		Revision as of 18:15, 26 February 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4ybu is ~~ON HOLD until Feb 24 2017~~	+	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom - 1st cycle==
-		+	<StructureSection load='4ybu' size='340' side='right' caption='[[4ybu]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~Authors~~: ~~Nosrati~~, M., ~~Geiger~~, J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ybu]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YBU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YBU FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[2g7b\|2g7b]], [[4i9r\|4i9r]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]]</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=4ybu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ybu OCA], [http://pdbe.org/4ybu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ybu RCSB], [http://www.ebi.ac.uk/pdbsum/4ybu PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RABP2_HUMAN RABP2_HUMAN]] Transports retinoic acid to the nucleus. Regulates the access of retinoic acid to the nuclear retinoic acid receptors.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Geiger, J]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]
-	[[Category: ~~Geiger, J~~]]	+	[[Category: Photoswitchable protein]]
		+	[[Category: Protein engineering]]
		+	[[Category: Retinal iminium pka change by isomerization]]
		+	[[Category: Retinal isomerization]]
		+	[[Category: Retinal psb]]
		+	[[Category: Transport protein]]

OCA at 13:40, 13 January 2016

OCA — Wed, 13 Jan 2016 13:40:01 GMT

←Older revision		Revision as of 13:40, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ybu is ON HOLD until ~~Paper Publication~~	+	The entry 4ybu is ON HOLD until Feb 24 2017

	Authors: Nosrati, M., Geiger, J.		Authors: Nosrati, M., Geiger, J.

OCA at 10:34, 18 March 2015

OCA — Wed, 18 Mar 2015 10:34:42 GMT

←Older revision		Revision as of 10:34, 18 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4ybu is ON HOLD	+	The entry 4ybu is ON HOLD until Paper Publication

	Authors: Nosrati, M., Geiger, J.		Authors: Nosrati, M., Geiger, J.

OCA at 10:17, 4 March 2015

OCA — Wed, 04 Mar 2015 10:17:01 GMT

←Older revision		Revision as of 10:17, 4 March 2015
Line 5:		Line 5:
	Authors: Nosrati, M., Geiger, J.		Authors: Nosrati, M., Geiger, J.

-	Description: Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom -1st cycle	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]
	[[Category: Geiger, J]]		[[Category: Geiger, J]]

OCA: Protected "4ybu" [edit=sysop:move=sysop]

OCA — Wed, 25 Feb 2015 12:57:47 GMT

Protected "4ybu" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:57, 25 February 2015