4ych - Revision history

OCA at 07:56, 27 September 2023

2023-09-27T07:56:43Z

←Older revision		Revision as of 07:56, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ych]] 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=4YCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YCH FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ych]] 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=4YCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YCH 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]] 1.96Å</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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [https://pdbe.org/4ych PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [https://www.ebi.ac.uk/pdbsum/4ych PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych 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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [https://pdbe.org/4ych PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [https://www.ebi.ac.uk/pdbsum/4ych PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:08, 3 May 2023

2023-05-03T08:08:26Z

←Older revision		Revision as of 08:08, 3 May 2023
Line 3:		Line 3:
	<StructureSection load='4ych' size='340' side='right'caption='[[4ych]], [[Resolution\|resolution]] 1.96Å' scene=''>		<StructureSection load='4ych' size='340' side='right'caption='[[4ych]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ych]] 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=4YCH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YCH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ych]] 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=4YCH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YCH 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]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [https://pdbe.org/4ych PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [https://www.ebi.ac.uk/pdbsum/4ych PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych 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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [~~http~~://pdbe.org/4ych PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ych PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych 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: Photo switchable protein]]~~	+
-	~~[[Category: Protein engineering]]~~	+
-	~~[[Category: Retinal isomerization]]~~	+
-	~~[[Category: Retinal psb pka change]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 07:22, 12 June 2019

2019-06-12T07:22:30Z

←Older revision		Revision as of 07:22, 12 June 2019
Line 1:		Line 1:

	==Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII with Retinal at 1.96 Angstrom - UV irradiated Crystal for 1 hour - 2nd cycle==		==Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII with Retinal at 1.96 Angstrom - UV irradiated Crystal for 1 hour - 2nd cycle==
-	<StructureSection load='4ych' size='340' side='right' caption='[[4ych]], [[Resolution\|resolution]] 1.96Å' scene=''>	+	<StructureSection load='4ych' size='340' side='right'caption='[[4ych]], [[Resolution\|resolution]] 1.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ych]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YCH FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ych]] 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=4YCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YCH 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]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [http://pdbe.org/4ych PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [http://www.ebi.ac.uk/pdbsum/4ych PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych 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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [http://pdbe.org/4ych PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [http://www.ebi.ac.uk/pdbsum/4ych PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4ych" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4ych" 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 18:38, 12 July 2016

2016-07-12T18:38:49Z

←Older revision		Revision as of 18:38, 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]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [http://pdbe.org/4ych PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [http://www.ebi.ac.uk/pdbsum/4ych 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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [http://pdbe.org/4ych PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [http://www.ebi.ac.uk/pdbsum/4ych PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ych 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 4ych" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 18:15, 26 February 2016

2016-02-26T18:15:46Z

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

-	~~The entry~~ 4ych is ~~ON HOLD until Feb 24 2017~~	+	==Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII with Retinal at 1.96 Angstrom - UV irradiated Crystal for 1 hour - 2nd cycle==
-		+	<StructureSection load='4ych' size='340' side='right' caption='[[4ych]], [[Resolution\|resolution]] 1.96Å' scene=''>
-	~~Authors~~: ~~Nosrati~~, M., ~~Geiger~~, J.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4ych]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YCH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YCH 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]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[2g7b\|2g7b]], [[4eej\|4eej]], [[4ybu\|4ybu]], [[4yce\|4yce]]</td></tr>
-	[[Category: Geiger, J.H]]	+	<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=4ych FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ych OCA], [http://pdbe.org/4ych PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ych RCSB], [http://www.ebi.ac.uk/pdbsum/4ych 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 H]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]
		+	[[Category: Photo switchable protein]]
		+	[[Category: Protein engineering]]
		+	[[Category: Retinal isomerization]]
		+	[[Category: Retinal psb pka change]]
		+	[[Category: Transport protein]]

OCA at 13:40, 13 January 2016

2016-01-13T13:40:58Z

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

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

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

OCA at 10:18, 4 March 2015

2015-03-04T10:18:00Z

←Older revision		Revision as of 10:18, 4 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

-	Description: ~~Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII with Retinal at 1.96 Angstrom -UV irradiated Crystal for 1 hour -2nd cycle~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Geiger, J.H]]		[[Category: Geiger, J.H]]
	[[Category: Nosrati, M]]		[[Category: Nosrati, M]]

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

2015-02-25T12:59:23Z

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

←Older revision

Revision as of 12:59, 25 February 2015

OCA: New page: '''Unreleased structure''' The entry 4ych is ON HOLD Authors: Nosrati, M., Geiger, J.H. Description: Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Reti...

2015-02-25T12:59:22Z

New page: '''Unreleased structure''' The entry 4ych is ON HOLD Authors: Nosrati, M., Geiger, J.H. Description: Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Reti...

New page

'''Unreleased structure'''

The entry 4ych is ON HOLD

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

Description: Crystal Structure of R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII with Retinal at 1.96 Angstrom -UV irradiated Crystal for 1 hour -2nd cycle
[[Category: Unreleased Structures]]
[[Category: Geiger, J.H]]
[[Category: Nosrati, M]]