6yxb - Revision history

OCA at 13:37, 24 January 2024

2024-01-24T13:37:48Z

←Older revision		Revision as of 13:37, 24 January 2024
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	<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yxb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Chlad Chlad~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yxb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chloroflexus_aggregans_DSM_9485 Chloroflexus aggregans DSM 9485]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.5Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[6rhf\|6rhf]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">Cagg_3753 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=326427 CHLAD])~~</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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb 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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B8GAY9_CHLAD B8GAY9_CHLAD]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Chlad~~]]	+	[[Category: Chloroflexus aggregans DSM 9485]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gushchin, I]]	+	[[Category: Gushchin I]]
-	[[Category: Kovalev, K]]	+	[[Category: Kovalev K]]
-	[[Category: Nazarenko, V]]	+	[[Category: Nazarenko V]]
-	[[Category: Remeeva, A]]	+	[[Category: Remeeva A]]
-	~~[[Category: Fluorescent protein]]~~	+
-	~~[[Category: Lov domain~~]]	+

OCA at 09:09, 21 July 2021

2021-07-21T09:09:01Z

←Older revision		Revision as of 09:09, 21 July 2021
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	<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yxb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yxb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Chlad Chlad]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[6rhf\|6rhf]]</div></td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6rhf\|6rhf]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Cagg_3753 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=326427 CHLAD])</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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb 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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb ProSAT]</span></td></tr>
	</table>		</table>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Chlad]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gushchin, I]]		[[Category: Gushchin, I]]

OCA at 05:29, 28 April 2021

2021-04-28T05:29:42Z

←Older revision		Revision as of 05:29, 28 April 2021
Line 1:		Line 1:

	==Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)==		==Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)==
-	<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]]' scene=''>	+	<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]], [[Resolution\|resolution]] 1.50Å' 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=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yxb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>
-	</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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb 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=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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;'>[[6rhf\|6rhf]]</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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Photoactive biological systems modify the optical properties of their chromophores, known as spectral tuning. Determining the molecular origin of spectral tuning is instrumental for understanding function and developing applications of these biomolecules. Spectral tuning in flavin-binding fluorescent proteins (FbFPs), an emerging class of fluorescent reporters, is limited by their dependency on protein-bound flavins, whose structure and hence electronic properties cannot be altered by mutation. A blue-shifted variant of the plant-derived iLOV FbFP has been created by introducing a lysine within the flavin-binding pocket, but the molecular basis of this shift remains unconfirmed. We here structurally characterize the blue-shifted iLOV variant and construct a new blue-shifted CagFbFP protein by introducing an analogous mutation. X-ray structures of both proteins reveal displacement of the lysine away from the chromophore and opening up of the structure as instrumental for the blue shift. Site saturation mutagenesis and high-throughput screening yielded a red-shifted variant, and structural analysis revealed that the lysine side chain of the blue-shifted variant is stabilized close to the flavin by a secondary mutation, accounting for the red shift. Thus, a single additional mutation in a blue-shifted variant is sufficient to generate a red-shifted FbFP. Using spectroscopy, X-ray crystallography and quantum mechanics molecular mechanics calculations, we provide a firm structural and functional understanding of spectral tuning in FbFPs. We also show that the identified blue- and red-shifted variants allow for two-color microscopy based on spectral separation. In summary, the generated blue- and red-shifted variants represent promising new tools for application in life sciences.
		+
		+	The molecular basis of spectral tuning in blue- and red-shifted flavin-binding fluorescent proteins.,Rollen K, Granzin J, Remeeva A, Davari MD, Gensch T, Nazarenko VV, Kovalev K, Bogorodskiy A, Borshchevskiy V, Hemmer S, Schwaneberg U, Gordeliy V, Jaeger KE, Batra-Safferling R, Gushchin I, Krauss U J Biol Chem. 2021 Apr 13:100662. doi: 10.1016/j.jbc.2021.100662. PMID:33862085<ref>PMID:33862085</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yxb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gushchin I]]	+	[[Category: Gushchin, I]]
-	[[Category: Kovalev K]]	+	[[Category: Kovalev, K]]
-	[[Category: Nazarenko V]]	+	[[Category: Nazarenko, V]]
-	[[Category: Remeeva A]]	+	[[Category: Remeeva, A]]
		+	[[Category: Fluorescent protein]]
		+	[[Category: Lov domain]]

OCA at 08:21, 21 April 2021

2021-04-21T08:21:02Z

←Older revision		Revision as of 08:21, 21 April 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yxb is ON HOLD until Paper Publication~~	+	==Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)==
-		+	<StructureSection load='6yxb' size='340' side='right'caption='[[6yxb]]' scene=''>
-	~~Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YXB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YXB FirstGlance]. <br>
-	~~Description:~~ Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)	+	</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=6yxb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yxb OCA], [https://pdbe.org/6yxb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yxb RCSB], [https://www.ebi.ac.uk/pdbsum/6yxb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yxb ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Nazarenko~~, V]]	+	__TOC__
-	[[Category: Gushchin, I]]	+	</StructureSection>
-	[[Category: Kovalev, K]]	+	[[Category: Large Structures]]
-	[[Category: Remeeva, A]]	+	[[Category: Gushchin I]]
		+	[[Category: Kovalev K]]
		+	[[Category: Nazarenko V]]
		+	[[Category: Remeeva A]]

OCA at 07:38, 22 July 2020

2020-07-22T07:38:22Z

←Older revision		Revision as of 07:38, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I.		Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I.
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	Description: Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)		Description: Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Nazarenko, V]]
	[[Category: Gushchin, I]]		[[Category: Gushchin, I]]
	[[Category: Kovalev, K]]		[[Category: Kovalev, K]]
	[[Category: Remeeva, A]]		[[Category: Remeeva, A]]
-	[[Category: Nazarenko, V]]

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

2020-05-06T04:50:08Z

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

←Older revision

Revision as of 04:50, 6 May 2020

OCA: New page: '''Unreleased structure''' The entry 6yxb is ON HOLD Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I. Description: Structure of Chloroflexus aggregans flavin based fluore...

2020-05-06T04:50:07Z

New page: '''Unreleased structure''' The entry 6yxb is ON HOLD Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I. Description: Structure of Chloroflexus aggregans flavin based fluore...

New page

'''Unreleased structure'''

The entry 6yxb is ON HOLD

Authors: Remeeva, A., Nazarenko, V., Kovalev, K., Gushchin, I.

Description: Structure of Chloroflexus aggregans flavin based fluorescent protein (CagFbFP) Q148K variant (space group P21)
[[Category: Unreleased Structures]]
[[Category: Gushchin, I]]
[[Category: Kovalev, K]]
[[Category: Remeeva, A]]
[[Category: Nazarenko, V]]