4yfr - Revision history

OCA at 07:59, 27 September 2023

2023-09-27T07:59:18Z

←Older revision		Revision as of 07:59, 27 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yfr]] 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=4YFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFR FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yfr]] 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=4YFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFR 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]] 1.952Å</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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [https://pdbe.org/4yfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [https://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr 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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [https://pdbe.org/4yfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [https://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:12, 3 May 2023

2023-05-03T08:12:32Z

←Older revision		Revision as of 08:12, 3 May 2023
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	<StructureSection load='4yfr' size='340' side='right'caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4yfr' size='340' side='right'caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yfr]] 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=4YFR OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YFR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yfr]] 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=4YFR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YFR 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]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [https://pdbe.org/4yfr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [https://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr 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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [~~http~~://pdbe.org/4yfr PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr 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 protonated schiff base pka change]]~~	+
-	~~[[Category: Transport protein~~]]	+

OCA at 06:42, 12 June 2019

2019-06-12T06:42:43Z

←Older revision		Revision as of 06:42, 12 June 2019
Line 1:		Line 1:

	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.95 Angstrom Resolution - UV irradiated crystal for 30 minutes - 1st Cycle==		==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.95 Angstrom Resolution - UV irradiated crystal for 30 minutes - 1st Cycle==
-	<StructureSection load='4yfr' size='340' side='right' caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='4yfr' size='340' side='right'caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yfr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yfr]] 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=4YFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFR 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]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [http://pdbe.org/4yfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [http://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr 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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [http://pdbe.org/4yfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [http://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr ProSAT]</span></td></tr>
	</table>		</table>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 4yfr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4yfr" 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 18:03, 12 July 2016

2016-07-12T18:03:21Z

←Older revision		Revision as of 18:03, 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]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4ybp\|4ybp]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [http://pdbe.org/4yfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [http://www.ebi.ac.uk/pdbsum/4yfr 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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [http://pdbe.org/4yfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [http://www.ebi.ac.uk/pdbsum/4yfr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yfr 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 4yfr" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 19:33, 9 March 2016

2016-03-09T19:33:21Z

←Older revision		Revision as of 19:33, 9 March 2016
Line 1:		Line 1:

-	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II with Retinal - UV irradiated crystal for 30 minutes - 1st Cycle==	+	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.95 Angstrom Resolution - UV irradiated crystal for 30 minutes - 1st Cycle==
	<StructureSection load='4yfr' size='340' side='right' caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='4yfr' size='340' side='right' caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 15:18, 2 March 2016

2016-03-02T15:18:02Z

←Older revision		Revision as of 15:18, 2 March 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 4yfr is ~~ON HOLD until Mar 02 2017~~	+	==Crystal structure of the R111K:Y134F:T54V:R132Q:P39Y:R59Y mutant of human Cellular Retinoic Acid Binding Protein II with Retinal - UV irradiated crystal for 30 minutes - 1st Cycle==
-		+	<StructureSection load='4yfr' size='340' side='right' caption='[[4yfr]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~Authors~~: ~~Nosrati~~, M., ~~Geiger~~, J.H.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4yfr]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YFR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YFR 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]], [[4ybu\|4ybu]], [[4i9s\|4i9s]], [[4ruu\|4ruu]], [[4eej\|4eej]], [[4yfp\|4yfp]], [[4yfq\|4yfq]]</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=4yfr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yfr OCA], [http://pdbe.org/4yfr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yfr RCSB], [http://www.ebi.ac.uk/pdbsum/4yfr 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 protonated schiff base pka change]]
		+	[[Category: Transport protein]]

OCA at 13:43, 13 January 2016

2016-01-13T13:43:41Z

←Older revision		Revision as of 13:43, 13 January 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4yfr is ON HOLD until ~~Paper Publication~~	+	The entry 4yfr is ON HOLD until Mar 02 2017

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

OCA at 10:34, 11 March 2015

2015-03-11T10:34:36Z

←Older revision		Revision as of 10:34, 11 March 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

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

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

2015-03-04T10:25:50Z

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

←Older revision

Revision as of 10:25, 4 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yfr is ON HOLD Authors: Nosrati, M., Geiger, J.H. Description: Category: Unreleased Structures Category: Geiger, J.H [[Category: Nosrati,...

2015-03-04T10:25:49Z

New page: '''Unreleased structure''' The entry 4yfr is ON HOLD Authors: Nosrati, M., Geiger, J.H. Description: Category: Unreleased Structures Category: Geiger, J.H [[Category: Nosrati,...

New page

'''Unreleased structure'''

The entry 4yfr is ON HOLD

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

Description:
[[Category: Unreleased Structures]]
[[Category: Geiger, J.H]]
[[Category: Nosrati, M]]