4rtc - Revision history

OCA at 17:55, 20 September 2023

2023-09-20T17:55:26Z

← Older revision		Revision as of 17:55, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RTC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RTC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 1.35Å</td></tr>
			<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [https://pdbe.org/4rtc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [https://www.ebi.ac.uk/pdbsum/4rtc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtc 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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [https://pdbe.org/4rtc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [https://www.ebi.ac.uk/pdbsum/4rtc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtc ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:27, 8 March 2023

2023-03-08T08:27:45Z

← Older revision		Revision as of 08:27, 8 March 2023
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	<StructureSection load='4rtc' size='340' side='right'caption='[[4rtc]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='4rtc' size='340' side='right'caption='[[4rtc]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Synthetic_construct_sequences~~ Synthetic construct ~~sequences~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4RTC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RTC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"~~><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	~~<tr~~ id~~='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class~~="~~sblockDat~~"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [https://pdbe.org/4rtc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [https://www.ebi.ac.uk/pdbsum/4rtc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtc ProSAT]</span></td></tr>
	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></~~td><td class="sblockDat"~~>~~[[2wso\|2wso]]~~</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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [~~http~~://pdbe.org/4rtc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4rtc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Synthetic construct ~~sequences~~]]		[[Category: Synthetic construct]]
	[[Category: Pletnev~~, S V~~]]		[[Category: Pletnev SV]]
	[[Category: Pletnev~~, V Z~~]]		[[Category: Pletnev VZ]]
	[[Category: Pletneva~~, N V]]~~		[[Category: Pletneva NV]]
	~~[[Category: Beta-barrel]]~~
	~~[[Category: Cerulean variant]]~~
	~~[[Category: Fluorescent protein]]~~
	~~[[Category: Nowgfp]]~~
	~~[[Category: Twg chromophore~~]]

OCA at 10:24, 1 May 2019

2019-05-01T10:24:41Z

← Older revision		Revision as of 10:24, 1 May 2019
Line 1:		Line 1:

	==Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0==		==Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0==
	<StructureSection load='4rtc' size='340' side='right' caption='[[4rtc]], [[Resolution\|resolution]] 1.35Å' scene=''>		<StructureSection load='4rtc' size='340' side='right'caption='[[4rtc]], [[Resolution\|resolution]] 1.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RTC FirstGlance]. <br>		<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RTC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wso\|2wso]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wso\|2wso]]</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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [http://www.ebi.ac.uk/pdbsum/4rtc 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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [http://pdbe.org/4rtc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [http://www.ebi.ac.uk/pdbsum/4rtc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rtc ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 4rtc" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
			[[Category: Synthetic construct sequences]]
	[[Category: Pletnev, S V]]		[[Category: Pletnev, S V]]
	[[Category: Pletnev, V Z]]		[[Category: Pletnev, V Z]]

OCA at 12:19, 2 September 2015

2015-09-02T12:19:28Z

← Older revision		Revision as of 12:19, 2 September 2015
Line 1:		Line 1:
	'''~~Unreleased~~ structure'''		==Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0==
			<StructureSection load='4rtc' size='340' side='right' caption='[[4rtc]], [[Resolution\|resolution]] 1.35Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[4rtc]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RTC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RTC FirstGlance]. <br>
			</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
			<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CRF:[(4Z)-2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(1H-INDOL-3-YLMETHYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC+ACID'>CRF</scene></td></tr>
			<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2wso\|2wso]]</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=4rtc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rtc OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4rtc RCSB], [http://www.ebi.ac.uk/pdbsum/4rtc PDBsum]</span></td></tr>
			</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			A green-emitting fluorescent variant, NowGFP, with a tryptophan-based chromophore (Thr65-Trp66-Gly67) was recently developed from the cyan mCerulean by introducing 18 point mutations. NowGFP is characterized by bright green fluorescence at physiological and higher pH and by weak cyan fluorescence at low pH. Illumination with blue light induces irreversible photoconversion of NowGFP from a green-emitting to a cyan-emitting form. Here, the X-ray structures of intact NowGFP at pH 9.0 and pH 4.8 and of its photoconverted variant, NowGFP_conv, are reported at 1.35, 1.18 and 2.5 A resolution, respectively. The structure of NowGFP at pH 9.0 suggests the anionic state of Trp66 of the chromophore to be the primary cause of its green fluorescence. At both examined pH values Trp66 predominantly adopted a cis conformation; only approximately 20% of the trans conformation was observed at pH 4.8. It was shown that Lys61, which adopts two distinct pH-dependent conformations, is a key residue playing a central role in chromophore ionization. At high pH the side chain of Lys61 forms two hydrogen bonds, one to the indole N atom of Trp66 and the other to the carboxyl group of the catalytic Glu222, enabling an indirect noncovalent connection between them that in turn promotes Trp66 deprotonation. At low pH, the side chain of Lys61 is directed away from Trp66 and forms a hydrogen bond to Gln207. It has been shown that photoconversion of NowGFP is accompanied by decomposition of Lys61, with a predominant cleavage of its side chain at the C(gamma)-C(delta) bond. Lys61, Glu222, Thr203 and Ser205 form a local hydrogen-bond network connected to the indole ring of the chromophore Trp66; mutation of any of these residues dramatically affects the spectral properties of NowGFP. On the other hand, an Ala150Val replacement in the vicinity of the chromophore indole ring resulted in a new advanced variant with a 2.5-fold improved photostability.

	~~The entry 4rtc is ON HOLD until Paper Publication~~		Structure of the green fluorescent protein NowGFP with an anionic tryptophan-based chromophore.,Pletnev VZ, Pletneva NV, Sarkisyan KS, Mishin AS, Lukyanov KA, Goryacheva EA, Ziganshin RH, Dauter Z, Pletnev S Acta Crystallogr D Biol Crystallogr. 2015 Aug 1;71(Pt 8):1699-707. doi:, 10.1107/S1399004715010159. Epub 2015 Jul 31. PMID:26249350<ref>PMID:26249350</ref>

	~~Authors: Pletnev~~, ~~V.Z~~.~~, Pletneva, N.V., Pletnev,~~ S.V.		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~Description: Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0~~		== References ==
	[[Category: ~~Unreleased Structures~~]]		<references/>
	[[Category: Pletnev, V.Z]]		__TOC__
	[[Category: Pletneva, N.V]]		</StructureSection>
	[[Category: ~~Pletnev, S.V~~]]		[[Category: Pletnev, S V]]
			[[Category: Pletnev, V Z]]
			[[Category: Pletneva, N V]]
			[[Category: Beta-barrel]]
			[[Category: Cerulean variant]]
			[[Category: Fluorescent protein]]
			[[Category: Nowgfp]]
			[[Category: Twg chromophore]]

OCA at 12:41, 7 February 2015

2015-02-07T12:41:07Z

← Older revision		Revision as of 12:41, 7 February 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 4rtc is ON HOLD		The entry 4rtc is ON HOLD until Paper Publication

	Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.		Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.

OCA at 17:20, 24 December 2014

2014-12-24T17:20:25Z

← Older revision		Revision as of 17:20, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0		Description: Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0
			[[Category: Unreleased Structures]]
			[[Category: Pletnev, V.Z]]
			[[Category: Pletneva, N.V]]
			[[Category: Pletnev, S.V]]

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

2014-11-26T06:46:38Z

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

← Older revision	Revision as of 06:46, 26 November 2014
(No difference)

OCA: New page: '''Unreleased structure''' The entry 4rtc is ON HOLD Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V. Description: Crystal structure of the green fluorescent variant, nowGFP, of t...

2014-11-26T06:46:37Z

New page: '''Unreleased structure''' The entry 4rtc is ON HOLD Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V. Description: Crystal structure of the green fluorescent variant, nowGFP, of t...

New page

'''Unreleased structure'''

The entry 4rtc is ON HOLD

Authors: Pletnev, V.Z., Pletneva, N.V., Pletnev, S.V.

Description: Crystal structure of the green fluorescent variant, nowGFP, of the cyan Cerulean at pH 9.0