6y8p - Revision history

OCA at 13:21, 24 January 2024

OCA — Wed, 24 Jan 2024 13:21:54 GMT

←Older revision		Revision as of 13:21, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6y8p' size='340' side='right'caption='[[6y8p]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6y8p' size='340' side='right'caption='[[6y8p]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6y8p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y8p]] 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=6Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8P FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGQ:[9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium'>OGQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGQ:[9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium'>OGQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p 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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/E5BBQ0_HUMAN E5BBQ0_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gotthard, G]]	+	[[Category: Gotthard G]]
-	[[Category: Hiblot, J]]	+	[[Category: Hiblot J]]
-	[[Category: Johnsson, K]]	+	[[Category: Johnsson K]]
-	[[Category: Tanzer, T]]	+	[[Category: Tanzer T]]
-	~~[[Category: Self-labeling protein]]~~	+
-	~~[[Category: Snap-tag]]~~	+
-	~~[[Category: Synthetic fluorophore]]~~	+
-	~~[[Category: Tetramethylrhodamine]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:56, 10 November 2021

OCA — Wed, 10 Nov 2021 07:56:04 GMT

←Older revision		Revision as of 07:56, 10 November 2021
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p 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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The self-labeling protein tags (SLPs) HaloTag7, SNAP-tag, and CLIP-tag allow the covalent labeling of fusion proteins with synthetic molecules for applications in bioimaging and biotechnology. To guide the selection of an SLP-substrate pair and provide guidelines for the design of substrates, we report a systematic and comparative study of the labeling kinetics and substrate specificities of HaloTag7, SNAP-tag, and CLIP-tag. HaloTag7 reaches almost diffusion-limited labeling rate constants with certain rhodamine substrates, which are more than 2 orders of magnitude higher than those of SNAP-tag for the corresponding substrates. SNAP-tag labeling rate constants, however, are less affected by the structure of the label than those of HaloTag7, which vary over 6 orders of magnitude for commonly employed substrates. Determining the crystal structures of HaloTag7 and SNAP-tag labeled with fluorescent substrates allowed us to rationalize their substrate preferences. We also demonstrate how these insights can be exploited to design substrates with improved labeling kinetics.
		+
		+	Kinetic and Structural Characterization of the Self-Labeling Protein Tags HaloTag7, SNAP-tag, and CLIP-tag.,Wilhelm J, Kuhn S, Tarnawski M, Gotthard G, Tunnermann J, Tanzer T, Karpenko J, Mertes N, Xue L, Uhrig U, Reinstein J, Hiblot J, Johnsson K Biochemistry. 2021 Aug 24;60(33):2560-2575. doi: 10.1021/acs.biochem.1c00258., Epub 2021 Aug 2. PMID:34339177<ref>PMID:34339177</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6y8p" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 15:48, 27 October 2021

OCA — Wed, 27 Oct 2021 15:48:46 GMT

←Older revision		Revision as of 15:48, 27 October 2021
Line 1:		Line 1:

	==Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore==		==Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore==
-	<StructureSection load='6y8p' size='340' side='right'caption='[[6y8p]]' scene=''>	+	<StructureSection load='6y8p' size='340' side='right'caption='[[6y8p]], [[Resolution\|resolution]] 2.30Å' 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=6Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8P FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6y8p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8P 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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=OGQ:[9-[2-carboxy-5-[(4-methylphenyl)methylcarbamoyl]phenyl]-6-(dimethylamino)xanthen-3-ylidene]-dimethyl-azanium'>OGQ</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gotthard G]]	+	[[Category: Gotthard, G]]
-	[[Category: Hiblot J]]	+	[[Category: Hiblot, J]]
-	[[Category: Johnsson K]]	+	[[Category: Johnsson, K]]
-	[[Category: Tanzer T]]	+	[[Category: Tanzer, T]]
		+	[[Category: Self-labeling protein]]
		+	[[Category: Snap-tag]]
		+	[[Category: Synthetic fluorophore]]
		+	[[Category: Tetramethylrhodamine]]
		+	[[Category: Transferase]]

OCA at 10:29, 31 March 2021

OCA — Wed, 31 Mar 2021 10:29:40 GMT

←Older revision		Revision as of 10:29, 31 March 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6y8p is ON HOLD until Mar 05 2022~~	+	==Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore==
-		+	<StructureSection load='6y8p' size='340' side='right'caption='[[6y8p]]' scene=''>
-	~~Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Y8P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Y8P FirstGlance]. <br>
-	~~Description:~~ Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore	+	</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=6y8p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6y8p OCA], [https://pdbe.org/6y8p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6y8p RCSB], [https://www.ebi.ac.uk/pdbsum/6y8p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6y8p ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Johnsson~~, K]]	+	__TOC__
-	[[Category: Gotthard, G]]	+	</StructureSection>
-	[[Category: Hiblot, J]]	+	[[Category: Large Structures]]
-	[[Category: Tanzer, T]]	+	[[Category: Gotthard G]]
		+	[[Category: Hiblot J]]
		+	[[Category: Johnsson K]]
		+	[[Category: Tanzer T]]

OCA at 08:31, 27 March 2020

OCA — Fri, 27 Mar 2020 08:31:49 GMT

←Older revision		Revision as of 08:31, 27 March 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6y8p is ON HOLD	+	The entry 6y8p is ON HOLD until Mar 05 2022

	Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J.		Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J.
Line 7:		Line 7:
	Description: Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore		Description: Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Gotthard, G]]
	[[Category: Johnsson, K]]		[[Category: Johnsson, K]]
		+	[[Category: Gotthard, G]]
	[[Category: Hiblot, J]]		[[Category: Hiblot, J]]
	[[Category: Tanzer, T]]		[[Category: Tanzer, T]]

OCA: Protected "6y8p" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2020 06:18:15 GMT

Protected "6y8p" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:18, 11 March 2020

OCA: New page: '''Unreleased structure''' The entry 6y8p is ON HOLD Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J. Description: Crystal structure of SNAP-tag labeled with a benzyl-tetram...

OCA — Wed, 11 Mar 2020 06:18:13 GMT

New page: '''Unreleased structure''' The entry 6y8p is ON HOLD Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J. Description: Crystal structure of SNAP-tag labeled with a benzyl-tetram...

New page

'''Unreleased structure'''

The entry 6y8p is ON HOLD

Authors: Gotthard, G., Tanzer, T., Johnsson, K., Hiblot, J.

Description: Crystal structure of SNAP-tag labeled with a benzyl-tetramethylrhodamine fluorophore
[[Category: Unreleased Structures]]
[[Category: Gotthard, G]]
[[Category: Johnsson, K]]
[[Category: Hiblot, J]]
[[Category: Tanzer, T]]